PRS Schizophrenia and PTSD with different parents.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "paperback-wrist",
   "metadata": {},
   "source": [
    "## Analysis for Schizophrenia"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 35,
   "id": "excess-student",
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 36,
   "id": "accurate-closing",
   "metadata": {},
   "outputs": [
    {
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       "      <th></th>\n",
       "      <th>CHR</th>\n",
       "      <th>SNP</th>\n",
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       "      <th>A1</th>\n",
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       "      <th>FRQ_A_56418</th>\n",
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       "      <th>HetISqt</th>\n",
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       "      <td>6</td>\n",
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       "      <td>T</td>\n",
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      "text/plain": [
       "         CHR            SNP        BP A1     A2  FRQ_A_56418  FRQ_U_78818  \\\n",
       "4553688    6  chr6:26518757  26518757  A      T      0.99300       0.9910   \n",
       "4584146    6    rs114476648  27633802  T      C      0.98100       0.9790   \n",
       "4802236    6  chr6:30332254  30332254  T      C      0.97300       0.9700   \n",
       "4565589    6     rs71559051  27799470  A      G      0.94500       0.9350   \n",
       "4559282    6    rs113780580  27555056  A  AACAC      0.94100       0.9300   \n",
       "...      ...            ...       ... ..    ...          ...          ...   \n",
       "4553584    6     rs71557345  26680698  A      G      0.06170       0.0734   \n",
       "4537686    6    rs192804591  27729706  A      T      0.06370       0.0756   \n",
       "4543692    6     rs35202262  27799514  T      C      0.06460       0.0766   \n",
       "4597569    6  chr6:27244243  27244243  T      C      0.02760       0.0311   \n",
       "4763487    6    rs114486118  30346826  T      C      0.00894       0.0104   \n",
       "\n",
       "          INFO       OR      SE             P  ngt Direction  HetISqt  HetDf  \\\n",
       "4553688  0.442  1.78229  0.1005  8.912000e-09    0  +???????      0.0      0   \n",
       "4584146  0.446  1.50606  0.0560  2.623000e-13    0  +???????      0.0      0   \n",
       "4802236  0.481  1.37355  0.0465  8.745000e-12    0  +???????      0.0      0   \n",
       "4565589  0.758  1.30918  0.0263  1.267000e-24    0  +???????      0.0      0   \n",
       "4559282  0.861  1.27813  0.0240  1.534000e-24    0  +???????      0.0      0   \n",
       "...        ...      ...     ...           ...  ...       ...      ...    ...   \n",
       "4553584  0.903  0.78671  0.0229  1.116000e-25    0  -???????      0.0      0   \n",
       "4537686  0.866  0.78568  0.0230  9.891000e-26    0  -???????      0.0      0   \n",
       "4543692  0.882  0.78553  0.0227  2.066000e-26    0  -???????      0.0      0   \n",
       "4597569  0.475  0.75828  0.0432  1.502000e-10    0  -???????      0.0      0   \n",
       "4763487  0.235  0.50535  0.1221  2.274000e-08    0  -???????      0.0      0   \n",
       "\n",
       "         HetPVa    Nca    Nco      Neff  \n",
       "4553688     1.0  33640  43456  37923.10  \n",
       "4584146     1.0  46945  59700  52551.45  \n",
       "4802236     1.0  33640  43456  37923.10  \n",
       "4565589     1.0  33640  43456  37923.10  \n",
       "4559282     1.0  33640  43456  37923.10  \n",
       "...         ...    ...    ...       ...  \n",
       "4553584     1.0  33640  43456  37923.10  \n",
       "4537686     1.0  33640  43456  37923.10  \n",
       "4543692     1.0  33640  43456  37923.10  \n",
       "4597569     1.0  46945  59700  52551.45  \n",
       "4763487     1.0  33640  43456  37923.10  \n",
       "\n",
       "[15445 rows x 19 columns]"
      ]
     },
     "execution_count": 36,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "schizophrenia_df = pd.read_csv(\"daner_natgen_eas_eur_autosomes\", sep='\\t')\n",
    "schizophrenia_df.sort_values('P',ascending= False)\n",
    "schizo_df_filt= schizophrenia_df.loc[schizophrenia_df['P']<=5e-8]\n",
    "schizo_df_filt.sort_values('OR',ascending= False)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 37,
   "id": "cosmetic-providence",
   "metadata": {},
   "outputs": [
    {
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       "      <th>HetISqt</th>\n",
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       "      <th>Nca</th>\n",
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       "      <td>0.306</td>\n",
       "      <td>0.958</td>\n",
       "      <td>1.09615</td>\n",
       "      <td>0.0105</td>\n",
       "      <td>2.884000e-18</td>\n",
       "      <td>2</td>\n",
       "      <td>++-+++++</td>\n",
       "      <td>32.1</td>\n",
       "      <td>7</td>\n",
       "      <td>0.17170</td>\n",
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       "      <th>6</th>\n",
       "      <td>2</td>\n",
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       "      <td>6.879000e-12</td>\n",
       "      <td>1</td>\n",
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       "      <td>0.0</td>\n",
       "      <td>6</td>\n",
       "      <td>0.89820</td>\n",
       "      <td>51274</td>\n",
       "      <td>64443</td>\n",
       "      <td>56864.72</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>5</td>\n",
       "      <td>rs2910032</td>\n",
       "      <td>152540354</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>0.579</td>\n",
       "      <td>0.545</td>\n",
       "      <td>0.963</td>\n",
       "      <td>0.94753</td>\n",
       "      <td>0.0093</td>\n",
       "      <td>5.968000e-09</td>\n",
       "      <td>25</td>\n",
       "      <td>-++++-+-</td>\n",
       "      <td>20.4</td>\n",
       "      <td>7</td>\n",
       "      <td>0.26810</td>\n",
       "      <td>56418</td>\n",
       "      <td>78818</td>\n",
       "      <td>64441.44</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>7</td>\n",
       "      <td>rs6461049</td>\n",
       "      <td>2017445</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>0.542</td>\n",
       "      <td>0.536</td>\n",
       "      <td>0.961</td>\n",
       "      <td>1.07691</td>\n",
       "      <td>0.0088</td>\n",
       "      <td>2.582000e-17</td>\n",
       "      <td>22</td>\n",
       "      <td>++-+++++</td>\n",
       "      <td>0.0</td>\n",
       "      <td>7</td>\n",
       "      <td>0.63360</td>\n",
       "      <td>56418</td>\n",
       "      <td>78818</td>\n",
       "      <td>64441.44</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>8</td>\n",
       "      <td>rs11995572</td>\n",
       "      <td>89592083</td>\n",
       "      <td>T</td>\n",
       "      <td>G</td>\n",
       "      <td>0.240</td>\n",
       "      <td>0.296</td>\n",
       "      <td>0.961</td>\n",
       "      <td>1.06481</td>\n",
       "      <td>0.0113</td>\n",
       "      <td>2.429000e-08</td>\n",
       "      <td>0</td>\n",
       "      <td>+--+++++</td>\n",
       "      <td>0.0</td>\n",
       "      <td>7</td>\n",
       "      <td>0.92030</td>\n",
       "      <td>56418</td>\n",
       "      <td>78818</td>\n",
       "      <td>64441.44</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>8</td>\n",
       "      <td>rs4129585</td>\n",
       "      <td>143312933</td>\n",
       "      <td>A</td>\n",
       "      <td>C</td>\n",
       "      <td>0.426</td>\n",
       "      <td>0.446</td>\n",
       "      <td>0.958</td>\n",
       "      <td>1.07047</td>\n",
       "      <td>0.0090</td>\n",
       "      <td>4.831000e-14</td>\n",
       "      <td>51</td>\n",
       "      <td>++--+++-</td>\n",
       "      <td>27.8</td>\n",
       "      <td>7</td>\n",
       "      <td>0.20620</td>\n",
       "      <td>56418</td>\n",
       "      <td>78818</td>\n",
       "      <td>64441.44</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>10</td>\n",
       "      <td>rs7085104</td>\n",
       "      <td>104628873</td>\n",
       "      <td>A</td>\n",
       "      <td>G</td>\n",
       "      <td>0.603</td>\n",
       "      <td>0.580</td>\n",
       "      <td>0.962</td>\n",
       "      <td>1.08426</td>\n",
       "      <td>0.0088</td>\n",
       "      <td>3.649000e-20</td>\n",
       "      <td>24</td>\n",
       "      <td>+-+--++-</td>\n",
       "      <td>60.9</td>\n",
       "      <td>7</td>\n",
       "      <td>0.01233</td>\n",
       "      <td>56418</td>\n",
       "      <td>78818</td>\n",
       "      <td>64441.44</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>10</td>\n",
       "      <td>rs17691888</td>\n",
       "      <td>18734528</td>\n",
       "      <td>A</td>\n",
       "      <td>G</td>\n",
       "      <td>0.181</td>\n",
       "      <td>0.261</td>\n",
       "      <td>0.934</td>\n",
       "      <td>0.91448</td>\n",
       "      <td>0.0139</td>\n",
       "      <td>1.495000e-10</td>\n",
       "      <td>2</td>\n",
       "      <td>-+------</td>\n",
       "      <td>0.0</td>\n",
       "      <td>7</td>\n",
       "      <td>0.98410</td>\n",
       "      <td>56418</td>\n",
       "      <td>78818</td>\n",
       "      <td>64441.44</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>12</td>\n",
       "      <td>rs11532322</td>\n",
       "      <td>123731423</td>\n",
       "      <td>A</td>\n",
       "      <td>G</td>\n",
       "      <td>0.321</td>\n",
       "      <td>0.348</td>\n",
       "      <td>0.958</td>\n",
       "      <td>1.09111</td>\n",
       "      <td>0.0094</td>\n",
       "      <td>2.141000e-20</td>\n",
       "      <td>0</td>\n",
       "      <td>+-++++++</td>\n",
       "      <td>16.8</td>\n",
       "      <td>7</td>\n",
       "      <td>0.29790</td>\n",
       "      <td>56418</td>\n",
       "      <td>78818</td>\n",
       "      <td>64441.44</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>12</td>\n",
       "      <td>rs1006737</td>\n",
       "      <td>2345295</td>\n",
       "      <td>A</td>\n",
       "      <td>G</td>\n",
       "      <td>0.312</td>\n",
       "      <td>0.368</td>\n",
       "      <td>0.962</td>\n",
       "      <td>1.10043</td>\n",
       "      <td>0.0106</td>\n",
       "      <td>1.848000e-19</td>\n",
       "      <td>30</td>\n",
       "      <td>+--+++-+</td>\n",
       "      <td>0.0</td>\n",
       "      <td>7</td>\n",
       "      <td>0.74140</td>\n",
       "      <td>56418</td>\n",
       "      <td>78818</td>\n",
       "      <td>64441.44</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>18</td>\n",
       "      <td>rs4801131</td>\n",
       "      <td>52752700</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>0.459</td>\n",
       "      <td>0.461</td>\n",
       "      <td>0.960</td>\n",
       "      <td>0.95180</td>\n",
       "      <td>0.0089</td>\n",
       "      <td>2.944000e-08</td>\n",
       "      <td>2</td>\n",
       "      <td>--+-+-+-</td>\n",
       "      <td>0.0</td>\n",
       "      <td>7</td>\n",
       "      <td>0.46360</td>\n",
       "      <td>56418</td>\n",
       "      <td>78818</td>\n",
       "      <td>64441.44</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "    CHR         SNP         BP A1 A2  FRQ_A_56418  FRQ_U_78818   INFO  \\\n",
       "9     1     rs14403  243663893  T  C        0.272        0.325  0.963   \n",
       "12    1   rs1198588   98552832  A  T        0.154        0.171  0.998   \n",
       "0     2   rs2949006  200715388  T  G        0.266        0.306  0.958   \n",
       "6     2    rs778371  233743109  A  G        0.703        0.649  0.956   \n",
       "8     3   rs4687552   52838402  T  C        0.648        0.637  0.990   \n",
       "4     5   rs2910032  152540354  T  C        0.579        0.545  0.963   \n",
       "5     7   rs6461049    2017445  T  C        0.542        0.536  0.961   \n",
       "1     8  rs11995572   89592083  T  G        0.240        0.296  0.961   \n",
       "3     8   rs4129585  143312933  A  C        0.426        0.446  0.958   \n",
       "7    10   rs7085104  104628873  A  G        0.603        0.580  0.962   \n",
       "10   10  rs17691888   18734528  A  G        0.181        0.261  0.934   \n",
       "2    12  rs11532322  123731423  A  G        0.321        0.348  0.958   \n",
       "13   12   rs1006737    2345295  A  G        0.312        0.368  0.962   \n",
       "11   18   rs4801131   52752700  T  C        0.459        0.461  0.960   \n",
       "\n",
       "         OR      SE             P  ngt Direction  HetISqt  HetDf   HetPVa  \\\n",
       "9   0.94064  0.0100  8.718000e-10   17  ----+---     10.9      7  0.34550   \n",
       "12  0.90150  0.0125  1.399000e-16   24  ----????      0.0      3  0.63580   \n",
       "0   1.09615  0.0105  2.884000e-18    2  ++-+++++     32.1      7  0.17170   \n",
       "6   0.93146  0.0103  6.879000e-12    1  ----+---      0.0      7  0.83140   \n",
       "8   1.05781  0.0093  1.715000e-09    2  ++-++++?      0.0      6  0.89820   \n",
       "4   0.94753  0.0093  5.968000e-09   25  -++++-+-     20.4      7  0.26810   \n",
       "5   1.07691  0.0088  2.582000e-17   22  ++-+++++      0.0      7  0.63360   \n",
       "1   1.06481  0.0113  2.429000e-08    0  +--+++++      0.0      7  0.92030   \n",
       "3   1.07047  0.0090  4.831000e-14   51  ++--+++-     27.8      7  0.20620   \n",
       "7   1.08426  0.0088  3.649000e-20   24  +-+--++-     60.9      7  0.01233   \n",
       "10  0.91448  0.0139  1.495000e-10    2  -+------      0.0      7  0.98410   \n",
       "2   1.09111  0.0094  2.141000e-20    0  +-++++++     16.8      7  0.29790   \n",
       "13  1.10043  0.0106  1.848000e-19   30  +--+++-+      0.0      7  0.74140   \n",
       "11  0.95180  0.0089  2.944000e-08    2  --+-+-+-      0.0      7  0.46360   \n",
       "\n",
       "      Nca    Nco      Neff  \n",
       "9   56418  78818  64441.44  \n",
       "12  48223  60717  53635.28  \n",
       "0   56418  78818  64441.44  \n",
       "6   56418  78818  64441.44  \n",
       "8   51274  64443  56864.72  \n",
       "4   56418  78818  64441.44  \n",
       "5   56418  78818  64441.44  \n",
       "1   56418  78818  64441.44  \n",
       "3   56418  78818  64441.44  \n",
       "7   56418  78818  64441.44  \n",
       "10  56418  78818  64441.44  \n",
       "2   56418  78818  64441.44  \n",
       "13  56418  78818  64441.44  \n",
       "11  56418  78818  64441.44  "
      ]
     },
     "execution_count": 37,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "schizo_snps= pd.read_csv(\"schizophrenia_snps.txt\", sep='\\t', names=['SNP'])\n",
    "schizo_df_final= schizo_df_filt.merge(schizo_snps, on=\"SNP\")\n",
    "schizo_df_final= schizo_df_final.sort_values('CHR',ascending=True)\n",
    "schizo_df_final"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "tired-billion",
   "metadata": {},
   "source": [
    "### Getting the final genotype for generated Offsprings"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 39,
   "id": "romance-pantyhose",
   "metadata": {},
   "outputs": [],
   "source": [
    "%%bash\n",
    "\n",
    "sed -i -e 's/0|1/1/g' -e 's/1|0/1/g' -e 's/0|0/0/g' -e 's/1|1/2/g' HG01357_NA18530_high_scz_1000_t.tsv "
   ]
  },
  {
   "cell_type": "markdown",
   "id": "miniature-decline",
   "metadata": {},
   "source": [
    "### Getting the Odds Ratio Data for Schizophrenia SNP's"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 43,
   "id": "ordinary-latitude",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Unnamed: 0</th>\n",
       "      <th>#CHROM</th>\n",
       "      <th>POS</th>\n",
       "      <th>SNP</th>\n",
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       "      <th>1</th>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>44440146</td>\n",
       "      <td>rs4660761</td>\n",
       "      <td>G</td>\n",
       "      <td>A</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
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       "      <td>98552832</td>\n",
       "      <td>rs1198588</td>\n",
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       "      <th>3</th>\n",
       "      <td>3</td>\n",
       "      <td>1</td>\n",
       "      <td>243663893</td>\n",
       "      <td>rs14403</td>\n",
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       "      <td>rs2949006</td>\n",
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       "      <td>2</td>\n",
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       "      <td>2</td>\n",
       "      <td>2</td>\n",
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       "      <td>2</td>\n",
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       "      <th>5</th>\n",
       "      <td>5</td>\n",
       "      <td>2</td>\n",
       "      <td>233743109</td>\n",
       "      <td>rs778371</td>\n",
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       "      <td>rs4687552</td>\n",
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       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>7</td>\n",
       "      <td>5</td>\n",
       "      <td>142780339</td>\n",
       "      <td>rs6189</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>8</td>\n",
       "      <td>5</td>\n",
       "      <td>152540354</td>\n",
       "      <td>rs2910032</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>...</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>9</td>\n",
       "      <td>6</td>\n",
       "      <td>35542476</td>\n",
       "      <td>rs3800373</td>\n",
       "      <td>C</td>\n",
       "      <td>A</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>...</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>10</td>\n",
       "      <td>7</td>\n",
       "      <td>2017445</td>\n",
       "      <td>rs6461049</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>...</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>11</td>\n",
       "      <td>7</td>\n",
       "      <td>24324879</td>\n",
       "      <td>rs16139</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>12</td>\n",
       "      <td>8</td>\n",
       "      <td>89592083</td>\n",
       "      <td>rs11995572</td>\n",
       "      <td>G</td>\n",
       "      <td>T</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>...</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>13</td>\n",
       "      <td>8</td>\n",
       "      <td>143312933</td>\n",
       "      <td>rs4129585</td>\n",
       "      <td>A</td>\n",
       "      <td>C</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>...</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>14</td>\n",
       "      <td>9</td>\n",
       "      <td>136500515</td>\n",
       "      <td>rs1611115</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>...</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>15</td>\n",
       "      <td>10</td>\n",
       "      <td>18734528</td>\n",
       "      <td>rs17691888</td>\n",
       "      <td>G</td>\n",
       "      <td>A</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>16</td>\n",
       "      <td>10</td>\n",
       "      <td>104628873</td>\n",
       "      <td>rs7085104</td>\n",
       "      <td>A</td>\n",
       "      <td>G</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>...</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>17</td>\n",
       "      <td>11</td>\n",
       "      <td>113270828</td>\n",
       "      <td>rs1800497</td>\n",
       "      <td>G</td>\n",
       "      <td>A</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>...</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>18</td>\n",
       "      <td>11</td>\n",
       "      <td>113283484</td>\n",
       "      <td>rs1801028</td>\n",
       "      <td>G</td>\n",
       "      <td>C</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>19</td>\n",
       "      <td>11</td>\n",
       "      <td>113296286</td>\n",
       "      <td>rs1079597</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>...</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20</th>\n",
       "      <td>20</td>\n",
       "      <td>11</td>\n",
       "      <td>113346251</td>\n",
       "      <td>rs1799732</td>\n",
       "      <td>T</td>\n",
       "      <td>TG</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>...</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21</th>\n",
       "      <td>21</td>\n",
       "      <td>12</td>\n",
       "      <td>2345295</td>\n",
       "      <td>rs1006737</td>\n",
       "      <td>G</td>\n",
       "      <td>A</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22</th>\n",
       "      <td>22</td>\n",
       "      <td>12</td>\n",
       "      <td>123731423</td>\n",
       "      <td>rs11532322</td>\n",
       "      <td>A</td>\n",
       "      <td>G</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>...</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>23</th>\n",
       "      <td>23</td>\n",
       "      <td>13</td>\n",
       "      <td>47471478</td>\n",
       "      <td>rs6311</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>24</th>\n",
       "      <td>24</td>\n",
       "      <td>15</td>\n",
       "      <td>72640388</td>\n",
       "      <td>rs76173977</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>25</th>\n",
       "      <td>25</td>\n",
       "      <td>15</td>\n",
       "      <td>72642925</td>\n",
       "      <td>rs121907970</td>\n",
       "      <td>G</td>\n",
       "      <td>A</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>26</th>\n",
       "      <td>26</td>\n",
       "      <td>18</td>\n",
       "      <td>52752700</td>\n",
       "      <td>rs4801131</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>...</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>27 rows × 1008 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "    Unnamed: 0  #CHROM        POS          SNP REF ALT  HG01357  NA18530  \\\n",
       "0            0       1   44438974       rs7161   C   T        1        1   \n",
       "1            1       1   44440146    rs4660761   G   A        1        1   \n",
       "2            2       1   98552832    rs1198588   A   T        2        2   \n",
       "3            3       1  243663893      rs14403   C   T        0        1   \n",
       "4            4       2  200715388    rs2949006   T   G        2        2   \n",
       "5            5       2  233743109     rs778371   A   G        1        0   \n",
       "6            6       3   52838402    rs4687552   T   C        2        1   \n",
       "7            7       5  142780339       rs6189   C   T        0        0   \n",
       "8            8       5  152540354    rs2910032   C   T        2        2   \n",
       "9            9       6   35542476    rs3800373   C   A        2        1   \n",
       "10          10       7    2017445    rs6461049   C   T        1        2   \n",
       "11          11       7   24324879      rs16139   T   C        0        0   \n",
       "12          12       8   89592083   rs11995572   G   T        1        1   \n",
       "13          13       8  143312933    rs4129585   A   C        2        2   \n",
       "14          14       9  136500515    rs1611115   T   C        1        2   \n",
       "15          15      10   18734528   rs17691888   G   A        0        0   \n",
       "16          16      10  104628873    rs7085104   A   G        1        2   \n",
       "17          17      11  113270828    rs1800497   G   A        0        2   \n",
       "18          18      11  113283484    rs1801028   G   C        0        0   \n",
       "19          19      11  113296286    rs1079597   C   T        0        2   \n",
       "20          20      11  113346251    rs1799732   T  TG        2        2   \n",
       "21          21      12    2345295    rs1006737   G   A        1        0   \n",
       "22          22      12  123731423   rs11532322   A   G        2        2   \n",
       "23          23      13   47471478       rs6311   C   T        0        1   \n",
       "24          24      15   72640388   rs76173977   C   T        0        0   \n",
       "25          25      15   72642925  rs121907970   G   A        0        0   \n",
       "26          26      18   52752700    rs4801131   C   T        2        2   \n",
       "\n",
       "    OS_0  OS_1  ...  OS_990  OS_991  OS_992  OS_993  OS_994  OS_995  OS_996  \\\n",
       "0      1     0  ...       2       1       0       1       1       2       0   \n",
       "1      1     0  ...       2       1       0       1       1       2       0   \n",
       "2      2     2  ...       2       2       2       2       2       2       2   \n",
       "3      0     1  ...       0       1       0       1       0       0       1   \n",
       "4      2     2  ...       2       2       2       2       2       2       2   \n",
       "5      1     0  ...       1       1       1       1       0       0       1   \n",
       "6      1     2  ...       1       1       1       1       1       1       2   \n",
       "7      0     0  ...       0       0       0       0       0       0       0   \n",
       "8      2     2  ...       2       2       2       2       2       2       2   \n",
       "9      2     1  ...       1       2       1       2       1       1       1   \n",
       "10     2     2  ...       1       1       1       2       2       2       1   \n",
       "11     0     0  ...       0       0       0       0       0       0       0   \n",
       "12     1     1  ...       2       1       2       0       1       1       1   \n",
       "13     2     2  ...       2       2       2       2       2       2       2   \n",
       "14     2     2  ...       2       1       1       1       2       2       2   \n",
       "15     0     0  ...       0       0       0       0       0       0       0   \n",
       "16     1     1  ...       1       2       1       2       1       2       2   \n",
       "17     1     1  ...       1       1       1       1       1       1       1   \n",
       "18     0     0  ...       0       0       0       0       0       0       0   \n",
       "19     1     1  ...       1       1       1       1       1       1       1   \n",
       "20     2     2  ...       2       2       2       2       2       2       2   \n",
       "21     1     1  ...       0       1       0       0       1       0       0   \n",
       "22     2     2  ...       2       2       2       2       2       2       2   \n",
       "23     1     0  ...       0       0       0       1       0       0       1   \n",
       "24     0     0  ...       0       0       0       0       0       0       0   \n",
       "25     0     0  ...       0       0       0       0       0       0       0   \n",
       "26     2     2  ...       2       2       2       2       2       2       2   \n",
       "\n",
       "    OS_997  OS_998  OS_999  \n",
       "0        2       1       1  \n",
       "1        2       1       1  \n",
       "2        2       2       2  \n",
       "3        0       0       1  \n",
       "4        2       2       2  \n",
       "5        0       0       0  \n",
       "6        1       2       2  \n",
       "7        0       0       0  \n",
       "8        2       2       2  \n",
       "9        1       2       1  \n",
       "10       2       2       1  \n",
       "11       0       0       0  \n",
       "12       0       2       0  \n",
       "13       2       2       2  \n",
       "14       1       1       1  \n",
       "15       0       0       0  \n",
       "16       1       2       2  \n",
       "17       1       1       1  \n",
       "18       0       0       0  \n",
       "19       1       1       1  \n",
       "20       2       2       2  \n",
       "21       0       0       0  \n",
       "22       2       2       2  \n",
       "23       0       0       1  \n",
       "24       0       0       0  \n",
       "25       0       0       0  \n",
       "26       2       2       2  \n",
       "\n",
       "[27 rows x 1008 columns]"
      ]
     },
     "execution_count": 43,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "simulated_off = pd.read_csv(\"HG01357_NA18530_high_scz_1000_t.tsv\", sep='\\t')\n",
    "simulated_off = simulated_off.rename(columns = {'ID': 'SNP'}, inplace = False)\n",
    "simulated_off"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 44,
   "id": "included-medication",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
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       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>CHR</th>\n",
       "      <th>SNP</th>\n",
       "      <th>BP</th>\n",
       "      <th>A1</th>\n",
       "      <th>A2</th>\n",
       "      <th>FRQ_A_56418</th>\n",
       "      <th>FRQ_U_78818</th>\n",
       "      <th>INFO</th>\n",
       "      <th>OR</th>\n",
       "      <th>SE</th>\n",
       "      <th>...</th>\n",
       "      <th>OS_990</th>\n",
       "      <th>OS_991</th>\n",
       "      <th>OS_992</th>\n",
       "      <th>OS_993</th>\n",
       "      <th>OS_994</th>\n",
       "      <th>OS_995</th>\n",
       "      <th>OS_996</th>\n",
       "      <th>OS_997</th>\n",
       "      <th>OS_998</th>\n",
       "      <th>OS_999</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>1</td>\n",
       "      <td>rs14403</td>\n",
       "      <td>243663893</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>0.272</td>\n",
       "      <td>0.325</td>\n",
       "      <td>0.963</td>\n",
       "      <td>0.94064</td>\n",
       "      <td>0.0100</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>1</td>\n",
       "      <td>rs1198588</td>\n",
       "      <td>98552832</td>\n",
       "      <td>A</td>\n",
       "      <td>T</td>\n",
       "      <td>0.154</td>\n",
       "      <td>0.171</td>\n",
       "      <td>0.998</td>\n",
       "      <td>0.90150</td>\n",
       "      <td>0.0125</td>\n",
       "      <td>...</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>2</td>\n",
       "      <td>rs2949006</td>\n",
       "      <td>200715388</td>\n",
       "      <td>T</td>\n",
       "      <td>G</td>\n",
       "      <td>0.266</td>\n",
       "      <td>0.306</td>\n",
       "      <td>0.958</td>\n",
       "      <td>1.09615</td>\n",
       "      <td>0.0105</td>\n",
       "      <td>...</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>2</td>\n",
       "      <td>rs778371</td>\n",
       "      <td>233743109</td>\n",
       "      <td>A</td>\n",
       "      <td>G</td>\n",
       "      <td>0.703</td>\n",
       "      <td>0.649</td>\n",
       "      <td>0.956</td>\n",
       "      <td>0.93146</td>\n",
       "      <td>0.0103</td>\n",
       "      <td>...</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>3</td>\n",
       "      <td>rs4687552</td>\n",
       "      <td>52838402</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>0.648</td>\n",
       "      <td>0.637</td>\n",
       "      <td>0.990</td>\n",
       "      <td>1.05781</td>\n",
       "      <td>0.0093</td>\n",
       "      <td>...</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>5</td>\n",
       "      <td>rs2910032</td>\n",
       "      <td>152540354</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>0.579</td>\n",
       "      <td>0.545</td>\n",
       "      <td>0.963</td>\n",
       "      <td>0.94753</td>\n",
       "      <td>0.0093</td>\n",
       "      <td>...</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>7</td>\n",
       "      <td>rs6461049</td>\n",
       "      <td>2017445</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>0.542</td>\n",
       "      <td>0.536</td>\n",
       "      <td>0.961</td>\n",
       "      <td>1.07691</td>\n",
       "      <td>0.0088</td>\n",
       "      <td>...</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>8</td>\n",
       "      <td>rs11995572</td>\n",
       "      <td>89592083</td>\n",
       "      <td>T</td>\n",
       "      <td>G</td>\n",
       "      <td>0.240</td>\n",
       "      <td>0.296</td>\n",
       "      <td>0.961</td>\n",
       "      <td>1.06481</td>\n",
       "      <td>0.0113</td>\n",
       "      <td>...</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>8</td>\n",
       "      <td>rs4129585</td>\n",
       "      <td>143312933</td>\n",
       "      <td>A</td>\n",
       "      <td>C</td>\n",
       "      <td>0.426</td>\n",
       "      <td>0.446</td>\n",
       "      <td>0.958</td>\n",
       "      <td>1.07047</td>\n",
       "      <td>0.0090</td>\n",
       "      <td>...</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>10</td>\n",
       "      <td>rs7085104</td>\n",
       "      <td>104628873</td>\n",
       "      <td>A</td>\n",
       "      <td>G</td>\n",
       "      <td>0.603</td>\n",
       "      <td>0.580</td>\n",
       "      <td>0.962</td>\n",
       "      <td>1.08426</td>\n",
       "      <td>0.0088</td>\n",
       "      <td>...</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>10</td>\n",
       "      <td>rs17691888</td>\n",
       "      <td>18734528</td>\n",
       "      <td>A</td>\n",
       "      <td>G</td>\n",
       "      <td>0.181</td>\n",
       "      <td>0.261</td>\n",
       "      <td>0.934</td>\n",
       "      <td>0.91448</td>\n",
       "      <td>0.0139</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>12</td>\n",
       "      <td>rs11532322</td>\n",
       "      <td>123731423</td>\n",
       "      <td>A</td>\n",
       "      <td>G</td>\n",
       "      <td>0.321</td>\n",
       "      <td>0.348</td>\n",
       "      <td>0.958</td>\n",
       "      <td>1.09111</td>\n",
       "      <td>0.0094</td>\n",
       "      <td>...</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>12</td>\n",
       "      <td>rs1006737</td>\n",
       "      <td>2345295</td>\n",
       "      <td>A</td>\n",
       "      <td>G</td>\n",
       "      <td>0.312</td>\n",
       "      <td>0.368</td>\n",
       "      <td>0.962</td>\n",
       "      <td>1.10043</td>\n",
       "      <td>0.0106</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>18</td>\n",
       "      <td>rs4801131</td>\n",
       "      <td>52752700</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>0.459</td>\n",
       "      <td>0.461</td>\n",
       "      <td>0.960</td>\n",
       "      <td>0.95180</td>\n",
       "      <td>0.0089</td>\n",
       "      <td>...</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>14 rows × 1026 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "    CHR         SNP         BP A1 A2  FRQ_A_56418  FRQ_U_78818   INFO  \\\n",
       "0     1     rs14403  243663893  T  C        0.272        0.325  0.963   \n",
       "1     1   rs1198588   98552832  A  T        0.154        0.171  0.998   \n",
       "2     2   rs2949006  200715388  T  G        0.266        0.306  0.958   \n",
       "3     2    rs778371  233743109  A  G        0.703        0.649  0.956   \n",
       "4     3   rs4687552   52838402  T  C        0.648        0.637  0.990   \n",
       "5     5   rs2910032  152540354  T  C        0.579        0.545  0.963   \n",
       "6     7   rs6461049    2017445  T  C        0.542        0.536  0.961   \n",
       "7     8  rs11995572   89592083  T  G        0.240        0.296  0.961   \n",
       "8     8   rs4129585  143312933  A  C        0.426        0.446  0.958   \n",
       "9    10   rs7085104  104628873  A  G        0.603        0.580  0.962   \n",
       "10   10  rs17691888   18734528  A  G        0.181        0.261  0.934   \n",
       "11   12  rs11532322  123731423  A  G        0.321        0.348  0.958   \n",
       "12   12   rs1006737    2345295  A  G        0.312        0.368  0.962   \n",
       "13   18   rs4801131   52752700  T  C        0.459        0.461  0.960   \n",
       "\n",
       "         OR      SE  ...  OS_990  OS_991 OS_992  OS_993  OS_994  OS_995  \\\n",
       "0   0.94064  0.0100  ...       0       1      0       1       0       0   \n",
       "1   0.90150  0.0125  ...       2       2      2       2       2       2   \n",
       "2   1.09615  0.0105  ...       2       2      2       2       2       2   \n",
       "3   0.93146  0.0103  ...       1       1      1       1       0       0   \n",
       "4   1.05781  0.0093  ...       1       1      1       1       1       1   \n",
       "5   0.94753  0.0093  ...       2       2      2       2       2       2   \n",
       "6   1.07691  0.0088  ...       1       1      1       2       2       2   \n",
       "7   1.06481  0.0113  ...       2       1      2       0       1       1   \n",
       "8   1.07047  0.0090  ...       2       2      2       2       2       2   \n",
       "9   1.08426  0.0088  ...       1       2      1       2       1       2   \n",
       "10  0.91448  0.0139  ...       0       0      0       0       0       0   \n",
       "11  1.09111  0.0094  ...       2       2      2       2       2       2   \n",
       "12  1.10043  0.0106  ...       0       1      0       0       1       0   \n",
       "13  0.95180  0.0089  ...       2       2      2       2       2       2   \n",
       "\n",
       "    OS_996  OS_997  OS_998  OS_999  \n",
       "0        1       0       0       1  \n",
       "1        2       2       2       2  \n",
       "2        2       2       2       2  \n",
       "3        1       0       0       0  \n",
       "4        2       1       2       2  \n",
       "5        2       2       2       2  \n",
       "6        1       2       2       1  \n",
       "7        1       0       2       0  \n",
       "8        2       2       2       2  \n",
       "9        2       1       2       2  \n",
       "10       0       0       0       0  \n",
       "11       2       2       2       2  \n",
       "12       0       0       0       0  \n",
       "13       2       2       2       2  \n",
       "\n",
       "[14 rows x 1026 columns]"
      ]
     },
     "execution_count": 44,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "schizo_prs = schizo_df_final.merge(simulated_off, on='SNP')\n",
    "schizo_prs"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "understood-mortality",
   "metadata": {},
   "source": [
    "### Performing PRS Analysis for Schizophrenia"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 45,
   "id": "ruled-tactics",
   "metadata": {},
   "outputs": [],
   "source": [
    "column_names = schizo_prs.columns.to_list()\n",
    "column_names = column_names[24:]\n",
    "prs_individuals = []\n",
    "\n",
    "for individual in column_names:\n",
    "    schizo_prs['Score'] = schizo_prs.apply(lambda x: x[individual] * x['OR'], axis=1)\n",
    "    score = schizo_prs['Score'].sum()\n",
    "    list_item= [individual, score]\n",
    "    prs_individuals.append(list_item)\n",
    "    "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 46,
   "id": "settled-silver",
   "metadata": {},
   "outputs": [],
   "source": [
    "prs_ind_df = pd.DataFrame(prs_individuals, columns=['Individuals', 'Scores'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 47,
   "id": "sexual-updating",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Individuals</th>\n",
       "      <th>Scores</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>HG01357</td>\n",
       "      <td>19.49061</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>NA18530</td>\n",
       "      <td>19.50272</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>OS_0</td>\n",
       "      <td>19.50971</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>OS_1</td>\n",
       "      <td>20.57670</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>OS_2</td>\n",
       "      <td>21.52251</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>997</th>\n",
       "      <td>OS_995</td>\n",
       "      <td>18.56208</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>998</th>\n",
       "      <td>OS_996</td>\n",
       "      <td>20.41508</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>999</th>\n",
       "      <td>OS_997</td>\n",
       "      <td>16.41301</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1000</th>\n",
       "      <td>OS_998</td>\n",
       "      <td>20.68470</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1001</th>\n",
       "      <td>OS_999</td>\n",
       "      <td>18.41881</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>1002 rows × 2 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "     Individuals    Scores\n",
       "0        HG01357  19.49061\n",
       "1        NA18530  19.50272\n",
       "2           OS_0  19.50971\n",
       "3           OS_1  20.57670\n",
       "4           OS_2  21.52251\n",
       "...          ...       ...\n",
       "997       OS_995  18.56208\n",
       "998       OS_996  20.41508\n",
       "999       OS_997  16.41301\n",
       "1000      OS_998  20.68470\n",
       "1001      OS_999  18.41881\n",
       "\n",
       "[1002 rows x 2 columns]"
      ]
     },
     "execution_count": 47,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#prs_ind_df = prs_ind_df.rename(columns = {'0': 'Individuals', '1': 'Scores'}, inplace = False)\n",
    "prs_ind_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 48,
   "id": "competitive-snake",
   "metadata": {},
   "outputs": [],
   "source": [
    "# with open('final_prs_schizophrenia.txt', 'w') as filehandle:\n",
    "#     for listitem in prs_individuals:\n",
    "#         filehandle.write('%s\\n' % listitem)\n",
    "\n",
    "prs_ind_df.to_csv('final_prs_schizo_HG01357_NA18530_high.csv', encoding='utf-8')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "sacred-disabled",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "markdown",
   "id": "adopted-exploration",
   "metadata": {},
   "source": [
    "## Analysis for PTSD"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "id": "directed-chicago",
   "metadata": {},
   "outputs": [],
   "source": [
    "ptsd_df= pd.read_csv(\"SORTED_PTSD_EA9_AA7_LA1_SA2_ALL_study_specific_PCs1.txt\", sep='\\t')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "id": "greater-triangle",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
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       "\n",
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       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>RSID</th>\n",
       "      <th>Allele1</th>\n",
       "      <th>Allele2</th>\n",
       "      <th>Effect</th>\n",
       "      <th>StdErr</th>\n",
       "      <th>P-value</th>\n",
       "      <th>Direction</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>rs7400289</td>\n",
       "      <td>t</td>\n",
       "      <td>c</td>\n",
       "      <td>-0.2852</td>\n",
       "      <td>0.0525</td>\n",
       "      <td>5.491000e-08</td>\n",
       "      <td>+------?-+-----?+--</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>rs75117028</td>\n",
       "      <td>a</td>\n",
       "      <td>c</td>\n",
       "      <td>-0.3974</td>\n",
       "      <td>0.0744</td>\n",
       "      <td>9.088000e-08</td>\n",
       "      <td>+------?--+----?+++</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>chr13_70628410_D</td>\n",
       "      <td>d</td>\n",
       "      <td>i5</td>\n",
       "      <td>0.6437</td>\n",
       "      <td>0.1215</td>\n",
       "      <td>1.163000e-07</td>\n",
       "      <td>?????????-+++++??+-</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>rs149585529</td>\n",
       "      <td>a</td>\n",
       "      <td>g</td>\n",
       "      <td>0.6425</td>\n",
       "      <td>0.1215</td>\n",
       "      <td>1.242000e-07</td>\n",
       "      <td>?????????-+++++??+-</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>rs139558732</td>\n",
       "      <td>t</td>\n",
       "      <td>c</td>\n",
       "      <td>0.7161</td>\n",
       "      <td>0.1357</td>\n",
       "      <td>1.305000e-07</td>\n",
       "      <td>??????????+++++??+-</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>125270</th>\n",
       "      <td>rs6568886</td>\n",
       "      <td>t</td>\n",
       "      <td>c</td>\n",
       "      <td>0.8055</td>\n",
       "      <td>0.2870</td>\n",
       "      <td>5.000000e-03</td>\n",
       "      <td>+-??+-?????????????</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>125271</th>\n",
       "      <td>rs6829175</td>\n",
       "      <td>t</td>\n",
       "      <td>c</td>\n",
       "      <td>0.1508</td>\n",
       "      <td>0.0537</td>\n",
       "      <td>5.000000e-03</td>\n",
       "      <td>?????????++++++?+-+</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>125272</th>\n",
       "      <td>rs76146908</td>\n",
       "      <td>a</td>\n",
       "      <td>t</td>\n",
       "      <td>-0.1053</td>\n",
       "      <td>0.0375</td>\n",
       "      <td>5.000000e-03</td>\n",
       "      <td>---++--?++++---?+--</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>125273</th>\n",
       "      <td>rs79443596</td>\n",
       "      <td>t</td>\n",
       "      <td>g</td>\n",
       "      <td>0.1680</td>\n",
       "      <td>0.0598</td>\n",
       "      <td>5.000000e-03</td>\n",
       "      <td>++++++-+-+--+++-+-+</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>125274</th>\n",
       "      <td>rs993100</td>\n",
       "      <td>a</td>\n",
       "      <td>g</td>\n",
       "      <td>-0.5476</td>\n",
       "      <td>0.1951</td>\n",
       "      <td>5.000000e-03</td>\n",
       "      <td>?????????+-----??+?</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>125275 rows × 7 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                    RSID Allele1 Allele2  Effect  StdErr       P-value  \\\n",
       "0              rs7400289       t       c -0.2852  0.0525  5.491000e-08   \n",
       "1             rs75117028       a       c -0.3974  0.0744  9.088000e-08   \n",
       "2       chr13_70628410_D       d      i5  0.6437  0.1215  1.163000e-07   \n",
       "3            rs149585529       a       g  0.6425  0.1215  1.242000e-07   \n",
       "4            rs139558732       t       c  0.7161  0.1357  1.305000e-07   \n",
       "...                  ...     ...     ...     ...     ...           ...   \n",
       "125270         rs6568886       t       c  0.8055  0.2870  5.000000e-03   \n",
       "125271         rs6829175       t       c  0.1508  0.0537  5.000000e-03   \n",
       "125272        rs76146908       a       t -0.1053  0.0375  5.000000e-03   \n",
       "125273        rs79443596       t       g  0.1680  0.0598  5.000000e-03   \n",
       "125274          rs993100       a       g -0.5476  0.1951  5.000000e-03   \n",
       "\n",
       "                  Direction  \n",
       "0       +------?-+-----?+--  \n",
       "1       +------?--+----?+++  \n",
       "2       ?????????-+++++??+-  \n",
       "3       ?????????-+++++??+-  \n",
       "4       ??????????+++++??+-  \n",
       "...                     ...  \n",
       "125270  +-??+-?????????????  \n",
       "125271  ?????????++++++?+-+  \n",
       "125272  ---++--?++++---?+--  \n",
       "125273  ++++++-+-+--+++-+-+  \n",
       "125274  ?????????+-----??+?  \n",
       "\n",
       "[125275 rows x 7 columns]"
      ]
     },
     "execution_count": 19,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ptsd_df_filt= ptsd_df.loc[ptsd_df['P-value']<=5e-7]\n",
    "ptsd_df_filt = ptsd_df_filt.rename(columns = {'MarkerName': 'RSID'}, inplace = False)\n",
    "ptsd_df_filt"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "id": "physical-western",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
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       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>RSID</th>\n",
       "      <th>Allele1</th>\n",
       "      <th>Allele2</th>\n",
       "      <th>Effect</th>\n",
       "      <th>StdErr</th>\n",
       "      <th>P-value</th>\n",
       "      <th>Direction</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "Empty DataFrame\n",
       "Columns: [RSID, Allele1, Allele2, Effect, StdErr, P-value, Direction]\n",
       "Index: []"
      ]
     },
     "execution_count": 23,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ptsd_df_filt.loc[ptsd_df_filt['RSID']==\"rs6311\"]"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "danish-agent",
   "metadata": {},
   "source": [
    "### Getting PTSD SNP's"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "id": "amazing-azerbaijan",
   "metadata": {},
   "outputs": [],
   "source": [
    "all_snps = pd.read_csv(\"all_snps_data.txt\", sep='\\t')\n",
    "all_snps = all_snps.rename(columns = {'RSID': 'SNP'}, inplace = False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "id": "retired-helen",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
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       "\n",
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       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Chromosome</th>\n",
       "      <th>SNP</th>\n",
       "      <th>Disease_Name</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>22</th>\n",
       "      <td>11</td>\n",
       "      <td>rs1799732</td>\n",
       "      <td>PTSD</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>23</th>\n",
       "      <td>11</td>\n",
       "      <td>rs1801028</td>\n",
       "      <td>PTSD</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>24</th>\n",
       "      <td>11</td>\n",
       "      <td>rs1079597</td>\n",
       "      <td>PTSD</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>25</th>\n",
       "      <td>11</td>\n",
       "      <td>rs1800497</td>\n",
       "      <td>PTSD</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>26</th>\n",
       "      <td>17</td>\n",
       "      <td>rs4795541</td>\n",
       "      <td>PTSD</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>27</th>\n",
       "      <td>13</td>\n",
       "      <td>rs6311</td>\n",
       "      <td>PTSD</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>28</th>\n",
       "      <td>6</td>\n",
       "      <td>rs3800373</td>\n",
       "      <td>PTSD</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29</th>\n",
       "      <td>9</td>\n",
       "      <td>rs1611115</td>\n",
       "      <td>PTSD</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>30</th>\n",
       "      <td>7</td>\n",
       "      <td>rs16139</td>\n",
       "      <td>PTSD</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>31</th>\n",
       "      <td>5</td>\n",
       "      <td>rs6189</td>\n",
       "      <td>PTSD</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "    Chromosome        SNP Disease_Name\n",
       "22          11  rs1799732         PTSD\n",
       "23          11  rs1801028         PTSD\n",
       "24          11  rs1079597         PTSD\n",
       "25          11  rs1800497         PTSD\n",
       "26          17  rs4795541         PTSD\n",
       "27          13     rs6311         PTSD\n",
       "28           6  rs3800373         PTSD\n",
       "29           9  rs1611115         PTSD\n",
       "30           7    rs16139         PTSD\n",
       "31           5     rs6189         PTSD"
      ]
     },
     "execution_count": 17,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "all_snps_filt = all_snps.loc[all_snps['Disease_Name']=='PTSD']\n",
    "all_snps_filt"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "id": "yellow-bunch",
   "metadata": {},
   "outputs": [],
   "source": [
    "# ptsd_data = ptsd_df_filt.merge(all_snps, on='RSID')\n",
    "# ptsd_data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "id": "interracial-sugar",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "\n",
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       "\n",
       "    .dataframe thead th {\n",
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       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>CHR</th>\n",
       "      <th>SNP</th>\n",
       "      <th>BP</th>\n",
       "      <th>A1</th>\n",
       "      <th>A2</th>\n",
       "      <th>FRQ_A_29529</th>\n",
       "      <th>FRQ_U_166145</th>\n",
       "      <th>INFO</th>\n",
       "      <th>OR</th>\n",
       "      <th>SE</th>\n",
       "      <th>P</th>\n",
       "      <th>ngt</th>\n",
       "      <th>Direction</th>\n",
       "      <th>HetISqt</th>\n",
       "      <th>HetDf</th>\n",
       "      <th>HetPVa</th>\n",
       "      <th>Nca</th>\n",
       "      <th>Nco</th>\n",
       "      <th>Neff</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>6</td>\n",
       "      <td>rs9459288m</td>\n",
       "      <td>157790612</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>0.7144</td>\n",
       "      <td>0.7312</td>\n",
       "      <td>0.862271</td>\n",
       "      <td>0.915212</td>\n",
       "      <td>0.0170</td>\n",
       "      <td>1.804000e-07</td>\n",
       "      <td>0</td>\n",
       "      <td>--+---?-+---++-------+?+-----++-----?++++++---...</td>\n",
       "      <td>15.8</td>\n",
       "      <td>66</td>\n",
       "      <td>0.1415</td>\n",
       "      <td>18424</td>\n",
       "      <td>48144</td>\n",
       "      <td>46094.3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>13</td>\n",
       "      <td>rs57753395</td>\n",
       "      <td>99412436</td>\n",
       "      <td>A</td>\n",
       "      <td>G</td>\n",
       "      <td>0.0178</td>\n",
       "      <td>0.0133</td>\n",
       "      <td>0.905427</td>\n",
       "      <td>1.371220</td>\n",
       "      <td>0.0611</td>\n",
       "      <td>2.412000e-07</td>\n",
       "      <td>0</td>\n",
       "      <td>-?+?+-++??++++++++++++?+-+++??++-++?+--+-++-++...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>53</td>\n",
       "      <td>0.7344</td>\n",
       "      <td>25970</td>\n",
       "      <td>157806</td>\n",
       "      <td>77802.5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>13</td>\n",
       "      <td>rs73553233</td>\n",
       "      <td>99413222</td>\n",
       "      <td>A</td>\n",
       "      <td>G</td>\n",
       "      <td>0.0178</td>\n",
       "      <td>0.0134</td>\n",
       "      <td>0.905832</td>\n",
       "      <td>1.363430</td>\n",
       "      <td>0.0609</td>\n",
       "      <td>3.666000e-07</td>\n",
       "      <td>0</td>\n",
       "      <td>-?+?+-++??++++++++++++?+++++??++-++?+--+-++-++...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>53</td>\n",
       "      <td>0.7393</td>\n",
       "      <td>25970</td>\n",
       "      <td>157806</td>\n",
       "      <td>77802.5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>12</td>\n",
       "      <td>rs4078035</td>\n",
       "      <td>131887167</td>\n",
       "      <td>T</td>\n",
       "      <td>G</td>\n",
       "      <td>0.0519</td>\n",
       "      <td>0.0448</td>\n",
       "      <td>0.947899</td>\n",
       "      <td>1.191720</td>\n",
       "      <td>0.0348</td>\n",
       "      <td>4.597000e-07</td>\n",
       "      <td>4</td>\n",
       "      <td>+-+++-+-+---+++++-+++++-++-+--+-+++++-???????+...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>53</td>\n",
       "      <td>0.9893</td>\n",
       "      <td>24335</td>\n",
       "      <td>155025</td>\n",
       "      <td>73349.8</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>4</td>\n",
       "      <td>rs114981056</td>\n",
       "      <td>35761341</td>\n",
       "      <td>A</td>\n",
       "      <td>T</td>\n",
       "      <td>0.9641</td>\n",
       "      <td>0.9702</td>\n",
       "      <td>0.953328</td>\n",
       "      <td>0.814729</td>\n",
       "      <td>0.0408</td>\n",
       "      <td>5.079000e-07</td>\n",
       "      <td>1</td>\n",
       "      <td>-+------+---++---+-----+++-++---+-+--?????????...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>50</td>\n",
       "      <td>0.9216</td>\n",
       "      <td>25314</td>\n",
       "      <td>155596</td>\n",
       "      <td>75163.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9788616</th>\n",
       "      <td>9</td>\n",
       "      <td>rs4740906</td>\n",
       "      <td>7698716</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>0.6942</td>\n",
       "      <td>0.6953</td>\n",
       "      <td>0.986972</td>\n",
       "      <td>1.000000</td>\n",
       "      <td>0.0140</td>\n",
       "      <td>1.000000e+00</td>\n",
       "      <td>1</td>\n",
       "      <td>--++-+-+-+-++++-+-++-+--+---+++--+-+++--++-+-+...</td>\n",
       "      <td>17.4</td>\n",
       "      <td>69</td>\n",
       "      <td>0.1124</td>\n",
       "      <td>29529</td>\n",
       "      <td>166007</td>\n",
       "      <td>86058.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9788617</th>\n",
       "      <td>9</td>\n",
       "      <td>rs55880338</td>\n",
       "      <td>130629693</td>\n",
       "      <td>A</td>\n",
       "      <td>G</td>\n",
       "      <td>0.9767</td>\n",
       "      <td>0.9765</td>\n",
       "      <td>0.929439</td>\n",
       "      <td>1.000000</td>\n",
       "      <td>0.0544</td>\n",
       "      <td>1.000000e+00</td>\n",
       "      <td>4</td>\n",
       "      <td>-+-??++??-+--++-+++-+?++-???-+-?-+-+-++-+++--+...</td>\n",
       "      <td>3.4</td>\n",
       "      <td>57</td>\n",
       "      <td>0.4027</td>\n",
       "      <td>26247</td>\n",
       "      <td>160199</td>\n",
       "      <td>78937.8</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9788618</th>\n",
       "      <td>9</td>\n",
       "      <td>rs62548019</td>\n",
       "      <td>30521517</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>0.3924</td>\n",
       "      <td>0.3929</td>\n",
       "      <td>1.005880</td>\n",
       "      <td>1.000000</td>\n",
       "      <td>0.0149</td>\n",
       "      <td>1.000000e+00</td>\n",
       "      <td>1</td>\n",
       "      <td>+---+-+-+-++-+++----+++-++++++----++?+--+-+---...</td>\n",
       "      <td>13.3</td>\n",
       "      <td>68</td>\n",
       "      <td>0.1816</td>\n",
       "      <td>19167</td>\n",
       "      <td>50346</td>\n",
       "      <td>48018.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9788619</th>\n",
       "      <td>9</td>\n",
       "      <td>rs7856891</td>\n",
       "      <td>83932855</td>\n",
       "      <td>A</td>\n",
       "      <td>G</td>\n",
       "      <td>0.3421</td>\n",
       "      <td>0.3432</td>\n",
       "      <td>0.993334</td>\n",
       "      <td>1.000000</td>\n",
       "      <td>0.0138</td>\n",
       "      <td>1.000000e+00</td>\n",
       "      <td>1</td>\n",
       "      <td>--++-----+-++++--+-+--+-+--+-+--+-+-+-+--+-++-...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>69</td>\n",
       "      <td>0.7062</td>\n",
       "      <td>29529</td>\n",
       "      <td>166007</td>\n",
       "      <td>86058.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9788620</th>\n",
       "      <td>9</td>\n",
       "      <td>rs7871600</td>\n",
       "      <td>28940111</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>0.7810</td>\n",
       "      <td>0.7822</td>\n",
       "      <td>0.996311</td>\n",
       "      <td>1.000000</td>\n",
       "      <td>0.0157</td>\n",
       "      <td>1.000000e+00</td>\n",
       "      <td>28</td>\n",
       "      <td>-+++---+--+++-++--+--++++-++++-----+++++-+----...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>69</td>\n",
       "      <td>0.5795</td>\n",
       "      <td>29529</td>\n",
       "      <td>166007</td>\n",
       "      <td>86058.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>9788621 rows × 19 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "         CHR          SNP         BP A1 A2  FRQ_A_29529  FRQ_U_166145  \\\n",
       "0          6   rs9459288m  157790612  T  C       0.7144        0.7312   \n",
       "1         13   rs57753395   99412436  A  G       0.0178        0.0133   \n",
       "2         13   rs73553233   99413222  A  G       0.0178        0.0134   \n",
       "3         12    rs4078035  131887167  T  G       0.0519        0.0448   \n",
       "4          4  rs114981056   35761341  A  T       0.9641        0.9702   \n",
       "...      ...          ...        ... .. ..          ...           ...   \n",
       "9788616    9    rs4740906    7698716  T  C       0.6942        0.6953   \n",
       "9788617    9   rs55880338  130629693  A  G       0.9767        0.9765   \n",
       "9788618    9   rs62548019   30521517  T  C       0.3924        0.3929   \n",
       "9788619    9    rs7856891   83932855  A  G       0.3421        0.3432   \n",
       "9788620    9    rs7871600   28940111  T  C       0.7810        0.7822   \n",
       "\n",
       "             INFO        OR      SE             P  ngt  \\\n",
       "0        0.862271  0.915212  0.0170  1.804000e-07    0   \n",
       "1        0.905427  1.371220  0.0611  2.412000e-07    0   \n",
       "2        0.905832  1.363430  0.0609  3.666000e-07    0   \n",
       "3        0.947899  1.191720  0.0348  4.597000e-07    4   \n",
       "4        0.953328  0.814729  0.0408  5.079000e-07    1   \n",
       "...           ...       ...     ...           ...  ...   \n",
       "9788616  0.986972  1.000000  0.0140  1.000000e+00    1   \n",
       "9788617  0.929439  1.000000  0.0544  1.000000e+00    4   \n",
       "9788618  1.005880  1.000000  0.0149  1.000000e+00    1   \n",
       "9788619  0.993334  1.000000  0.0138  1.000000e+00    1   \n",
       "9788620  0.996311  1.000000  0.0157  1.000000e+00   28   \n",
       "\n",
       "                                                 Direction  HetISqt  HetDf  \\\n",
       "0        --+---?-+---++-------+?+-----++-----?++++++---...     15.8     66   \n",
       "1        -?+?+-++??++++++++++++?+-+++??++-++?+--+-++-++...      0.0     53   \n",
       "2        -?+?+-++??++++++++++++?+++++??++-++?+--+-++-++...      0.0     53   \n",
       "3        +-+++-+-+---+++++-+++++-++-+--+-+++++-???????+...      0.0     53   \n",
       "4        -+------+---++---+-----+++-++---+-+--?????????...      0.0     50   \n",
       "...                                                    ...      ...    ...   \n",
       "9788616  --++-+-+-+-++++-+-++-+--+---+++--+-+++--++-+-+...     17.4     69   \n",
       "9788617  -+-??++??-+--++-+++-+?++-???-+-?-+-+-++-+++--+...      3.4     57   \n",
       "9788618  +---+-+-+-++-+++----+++-++++++----++?+--+-+---...     13.3     68   \n",
       "9788619  --++-----+-++++--+-+--+-+--+-+--+-+-+-+--+-++-...      0.0     69   \n",
       "9788620  -+++---+--+++-++--+--++++-++++-----+++++-+----...      0.0     69   \n",
       "\n",
       "         HetPVa    Nca     Nco     Neff  \n",
       "0        0.1415  18424   48144  46094.3  \n",
       "1        0.7344  25970  157806  77802.5  \n",
       "2        0.7393  25970  157806  77802.5  \n",
       "3        0.9893  24335  155025  73349.8  \n",
       "4        0.9216  25314  155596  75163.0  \n",
       "...         ...    ...     ...      ...  \n",
       "9788616  0.1124  29529  166007  86058.0  \n",
       "9788617  0.4027  26247  160199  78937.8  \n",
       "9788618  0.1816  19167   50346  48018.0  \n",
       "9788619  0.7062  29529  166007  86058.0  \n",
       "9788620  0.5795  29529  166007  86058.0  \n",
       "\n",
       "[9788621 rows x 19 columns]"
      ]
     },
     "execution_count": 19,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ptsd_df_2 = pd.read_csv(\"pts_all_freeze2_overall.results\", sep='\\t')\n",
    "ptsd_df_2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "id": "placed-projection",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>CHR</th>\n",
       "      <th>SNP</th>\n",
       "      <th>BP</th>\n",
       "      <th>A1</th>\n",
       "      <th>A2</th>\n",
       "      <th>FRQ_A_29529</th>\n",
       "      <th>FRQ_U_166145</th>\n",
       "      <th>INFO</th>\n",
       "      <th>OR</th>\n",
       "      <th>SE</th>\n",
       "      <th>P</th>\n",
       "      <th>ngt</th>\n",
       "      <th>Direction</th>\n",
       "      <th>HetISqt</th>\n",
       "      <th>HetDf</th>\n",
       "      <th>HetPVa</th>\n",
       "      <th>Nca</th>\n",
       "      <th>Nco</th>\n",
       "      <th>Neff</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>6</td>\n",
       "      <td>rs9459288m</td>\n",
       "      <td>157790612</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>0.7144</td>\n",
       "      <td>0.7312</td>\n",
       "      <td>0.862271</td>\n",
       "      <td>0.915212</td>\n",
       "      <td>0.0170</td>\n",
       "      <td>1.804000e-07</td>\n",
       "      <td>0</td>\n",
       "      <td>--+---?-+---++-------+?+-----++-----?++++++---...</td>\n",
       "      <td>15.8</td>\n",
       "      <td>66</td>\n",
       "      <td>0.1415</td>\n",
       "      <td>18424</td>\n",
       "      <td>48144</td>\n",
       "      <td>46094.3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>13</td>\n",
       "      <td>rs57753395</td>\n",
       "      <td>99412436</td>\n",
       "      <td>A</td>\n",
       "      <td>G</td>\n",
       "      <td>0.0178</td>\n",
       "      <td>0.0133</td>\n",
       "      <td>0.905427</td>\n",
       "      <td>1.371220</td>\n",
       "      <td>0.0611</td>\n",
       "      <td>2.412000e-07</td>\n",
       "      <td>0</td>\n",
       "      <td>-?+?+-++??++++++++++++?+-+++??++-++?+--+-++-++...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>53</td>\n",
       "      <td>0.7344</td>\n",
       "      <td>25970</td>\n",
       "      <td>157806</td>\n",
       "      <td>77802.5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>13</td>\n",
       "      <td>rs73553233</td>\n",
       "      <td>99413222</td>\n",
       "      <td>A</td>\n",
       "      <td>G</td>\n",
       "      <td>0.0178</td>\n",
       "      <td>0.0134</td>\n",
       "      <td>0.905832</td>\n",
       "      <td>1.363430</td>\n",
       "      <td>0.0609</td>\n",
       "      <td>3.666000e-07</td>\n",
       "      <td>0</td>\n",
       "      <td>-?+?+-++??++++++++++++?+++++??++-++?+--+-++-++...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>53</td>\n",
       "      <td>0.7393</td>\n",
       "      <td>25970</td>\n",
       "      <td>157806</td>\n",
       "      <td>77802.5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>12</td>\n",
       "      <td>rs4078035</td>\n",
       "      <td>131887167</td>\n",
       "      <td>T</td>\n",
       "      <td>G</td>\n",
       "      <td>0.0519</td>\n",
       "      <td>0.0448</td>\n",
       "      <td>0.947899</td>\n",
       "      <td>1.191720</td>\n",
       "      <td>0.0348</td>\n",
       "      <td>4.597000e-07</td>\n",
       "      <td>4</td>\n",
       "      <td>+-+++-+-+---+++++-+++++-++-+--+-+++++-???????+...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>53</td>\n",
       "      <td>0.9893</td>\n",
       "      <td>24335</td>\n",
       "      <td>155025</td>\n",
       "      <td>73349.8</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   CHR         SNP         BP A1 A2  FRQ_A_29529  FRQ_U_166145      INFO  \\\n",
       "0    6  rs9459288m  157790612  T  C       0.7144        0.7312  0.862271   \n",
       "1   13  rs57753395   99412436  A  G       0.0178        0.0133  0.905427   \n",
       "2   13  rs73553233   99413222  A  G       0.0178        0.0134  0.905832   \n",
       "3   12   rs4078035  131887167  T  G       0.0519        0.0448  0.947899   \n",
       "\n",
       "         OR      SE             P  ngt  \\\n",
       "0  0.915212  0.0170  1.804000e-07    0   \n",
       "1  1.371220  0.0611  2.412000e-07    0   \n",
       "2  1.363430  0.0609  3.666000e-07    0   \n",
       "3  1.191720  0.0348  4.597000e-07    4   \n",
       "\n",
       "                                           Direction  HetISqt  HetDf  HetPVa  \\\n",
       "0  --+---?-+---++-------+?+-----++-----?++++++---...     15.8     66  0.1415   \n",
       "1  -?+?+-++??++++++++++++?+-+++??++-++?+--+-++-++...      0.0     53  0.7344   \n",
       "2  -?+?+-++??++++++++++++?+++++??++-++?+--+-++-++...      0.0     53  0.7393   \n",
       "3  +-+++-+-+---+++++-+++++-++-+--+-+++++-???????+...      0.0     53  0.9893   \n",
       "\n",
       "     Nca     Nco     Neff  \n",
       "0  18424   48144  46094.3  \n",
       "1  25970  157806  77802.5  \n",
       "2  25970  157806  77802.5  \n",
       "3  24335  155025  73349.8  "
      ]
     },
     "execution_count": 25,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ptsd_df_filt = ptsd_df_2.loc[ptsd_df_2['P']<=5e-7]\n",
    "ptsd_df_filt"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "rising-sister",
   "metadata": {},
   "source": [
    "### Getting the Odds Ratio Data for PTSD SNP's"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "id": "molecular-apparel",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "\n",
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       "\n",
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>CHR</th>\n",
       "      <th>SNP</th>\n",
       "      <th>BP</th>\n",
       "      <th>A1</th>\n",
       "      <th>A2</th>\n",
       "      <th>FRQ_A_29529</th>\n",
       "      <th>FRQ_U_166145</th>\n",
       "      <th>INFO</th>\n",
       "      <th>OR</th>\n",
       "      <th>SE</th>\n",
       "      <th>...</th>\n",
       "      <th>ngt</th>\n",
       "      <th>Direction</th>\n",
       "      <th>HetISqt</th>\n",
       "      <th>HetDf</th>\n",
       "      <th>HetPVa</th>\n",
       "      <th>Nca</th>\n",
       "      <th>Nco</th>\n",
       "      <th>Neff</th>\n",
       "      <th>Chromosome</th>\n",
       "      <th>Disease_Name</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>5</td>\n",
       "      <td>rs2910032</td>\n",
       "      <td>152540354</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>0.5023</td>\n",
       "      <td>0.5105</td>\n",
       "      <td>0.997635</td>\n",
       "      <td>0.957241</td>\n",
       "      <td>0.0127</td>\n",
       "      <td>...</td>\n",
       "      <td>10</td>\n",
       "      <td>-+-------+--+-++----++--+-+-+------+----++-+-+...</td>\n",
       "      <td>41.5</td>\n",
       "      <td>69</td>\n",
       "      <td>0.000223</td>\n",
       "      <td>29529</td>\n",
       "      <td>166007</td>\n",
       "      <td>86058.0</td>\n",
       "      <td>5</td>\n",
       "      <td>Schizophrenia</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>8</td>\n",
       "      <td>rs4129585</td>\n",
       "      <td>143312933</td>\n",
       "      <td>A</td>\n",
       "      <td>C</td>\n",
       "      <td>0.3996</td>\n",
       "      <td>0.3937</td>\n",
       "      <td>1.000940</td>\n",
       "      <td>1.034790</td>\n",
       "      <td>0.0135</td>\n",
       "      <td>...</td>\n",
       "      <td>68</td>\n",
       "      <td>-+-+-+-+-+++-++++-++++--+++++--+-++++++++++++-...</td>\n",
       "      <td>4.2</td>\n",
       "      <td>69</td>\n",
       "      <td>0.377500</td>\n",
       "      <td>29529</td>\n",
       "      <td>166007</td>\n",
       "      <td>86058.0</td>\n",
       "      <td>8</td>\n",
       "      <td>Schizophrenia</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>3</td>\n",
       "      <td>rs4687552</td>\n",
       "      <td>52838402</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>0.6551</td>\n",
       "      <td>0.6497</td>\n",
       "      <td>0.997296</td>\n",
       "      <td>1.030870</td>\n",
       "      <td>0.0132</td>\n",
       "      <td>...</td>\n",
       "      <td>6</td>\n",
       "      <td>+---+++-+++-+-+-+-+---+---+++--++++-++++--++++...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>69</td>\n",
       "      <td>0.541400</td>\n",
       "      <td>29529</td>\n",
       "      <td>166007</td>\n",
       "      <td>86058.0</td>\n",
       "      <td>3</td>\n",
       "      <td>Schizophrenia</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>1</td>\n",
       "      <td>rs14403</td>\n",
       "      <td>243663893</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>0.1968</td>\n",
       "      <td>0.2008</td>\n",
       "      <td>0.989069</td>\n",
       "      <td>0.963965</td>\n",
       "      <td>0.0162</td>\n",
       "      <td>...</td>\n",
       "      <td>15</td>\n",
       "      <td>---------++--++--+--+--+--++++++-------+--+--+...</td>\n",
       "      <td>11.5</td>\n",
       "      <td>69</td>\n",
       "      <td>0.215800</td>\n",
       "      <td>29529</td>\n",
       "      <td>166007</td>\n",
       "      <td>86058.0</td>\n",
       "      <td>1</td>\n",
       "      <td>Schizophrenia</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>11</td>\n",
       "      <td>rs1079597</td>\n",
       "      <td>113296286</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>0.1989</td>\n",
       "      <td>0.1941</td>\n",
       "      <td>0.998944</td>\n",
       "      <td>1.035210</td>\n",
       "      <td>0.0164</td>\n",
       "      <td>...</td>\n",
       "      <td>66</td>\n",
       "      <td>-++---++-+-+-+++-+++-+--+--++-++-+-++++-+--+++...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>69</td>\n",
       "      <td>0.999100</td>\n",
       "      <td>29529</td>\n",
       "      <td>166007</td>\n",
       "      <td>86058.0</td>\n",
       "      <td>11</td>\n",
       "      <td>PTSD</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>8</td>\n",
       "      <td>rs11995572</td>\n",
       "      <td>89592083</td>\n",
       "      <td>T</td>\n",
       "      <td>G</td>\n",
       "      <td>0.2577</td>\n",
       "      <td>0.2559</td>\n",
       "      <td>0.996287</td>\n",
       "      <td>1.017450</td>\n",
       "      <td>0.0160</td>\n",
       "      <td>...</td>\n",
       "      <td>1</td>\n",
       "      <td>+-+------++-+-+--+++++++----+-+-+-+-?-+-++--++...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>68</td>\n",
       "      <td>0.820000</td>\n",
       "      <td>19167</td>\n",
       "      <td>50346</td>\n",
       "      <td>48018.0</td>\n",
       "      <td>8</td>\n",
       "      <td>Schizophrenia</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>12</td>\n",
       "      <td>rs11532322</td>\n",
       "      <td>123731423</td>\n",
       "      <td>A</td>\n",
       "      <td>G</td>\n",
       "      <td>0.3552</td>\n",
       "      <td>0.3569</td>\n",
       "      <td>1.000640</td>\n",
       "      <td>0.985309</td>\n",
       "      <td>0.0145</td>\n",
       "      <td>...</td>\n",
       "      <td>1</td>\n",
       "      <td>++-+++-+++-+--+---++--+++---+-++++-+-++++-+---...</td>\n",
       "      <td>17.6</td>\n",
       "      <td>69</td>\n",
       "      <td>0.108500</td>\n",
       "      <td>29529</td>\n",
       "      <td>166007</td>\n",
       "      <td>86058.0</td>\n",
       "      <td>12</td>\n",
       "      <td>Schizophrenia</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>11</td>\n",
       "      <td>rs1800497</td>\n",
       "      <td>113270828</td>\n",
       "      <td>A</td>\n",
       "      <td>G</td>\n",
       "      <td>0.2659</td>\n",
       "      <td>0.2628</td>\n",
       "      <td>0.997417</td>\n",
       "      <td>1.014610</td>\n",
       "      <td>0.0146</td>\n",
       "      <td>...</td>\n",
       "      <td>46</td>\n",
       "      <td>-+++--++-+-+-+++--++-+-----++-++++-++++-+--+++...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>69</td>\n",
       "      <td>0.809400</td>\n",
       "      <td>29529</td>\n",
       "      <td>166007</td>\n",
       "      <td>86058.0</td>\n",
       "      <td>11</td>\n",
       "      <td>PTSD</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>5</td>\n",
       "      <td>rs6189</td>\n",
       "      <td>142780339</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>0.0275</td>\n",
       "      <td>0.0274</td>\n",
       "      <td>0.997180</td>\n",
       "      <td>1.042580</td>\n",
       "      <td>0.0444</td>\n",
       "      <td>...</td>\n",
       "      <td>35</td>\n",
       "      <td>++-++---+++-+-+-+-+-+-+--+-++++--+-++??????-??...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>48</td>\n",
       "      <td>0.720800</td>\n",
       "      <td>23581</td>\n",
       "      <td>152505</td>\n",
       "      <td>71272.5</td>\n",
       "      <td>5</td>\n",
       "      <td>PTSD</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>7</td>\n",
       "      <td>rs6461049</td>\n",
       "      <td>2017445</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>0.5505</td>\n",
       "      <td>0.5514</td>\n",
       "      <td>0.996514</td>\n",
       "      <td>0.988467</td>\n",
       "      <td>0.0127</td>\n",
       "      <td>...</td>\n",
       "      <td>63</td>\n",
       "      <td>--++---+-++++++++-----+--+-+++++-+----++-+-+--...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>69</td>\n",
       "      <td>0.797500</td>\n",
       "      <td>29529</td>\n",
       "      <td>166007</td>\n",
       "      <td>86058.0</td>\n",
       "      <td>7</td>\n",
       "      <td>Schizophrenia</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>10</td>\n",
       "      <td>rs17691888</td>\n",
       "      <td>18734528</td>\n",
       "      <td>A</td>\n",
       "      <td>G</td>\n",
       "      <td>0.1441</td>\n",
       "      <td>0.1473</td>\n",
       "      <td>0.959657</td>\n",
       "      <td>0.982751</td>\n",
       "      <td>0.0208</td>\n",
       "      <td>...</td>\n",
       "      <td>6</td>\n",
       "      <td>-+-+--+---++++-+----+-----+++-++--++?--++++++-...</td>\n",
       "      <td>6.5</td>\n",
       "      <td>68</td>\n",
       "      <td>0.326100</td>\n",
       "      <td>19167</td>\n",
       "      <td>50346</td>\n",
       "      <td>48018.0</td>\n",
       "      <td>10</td>\n",
       "      <td>Schizophrenia</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>2</td>\n",
       "      <td>rs778371</td>\n",
       "      <td>233743109</td>\n",
       "      <td>A</td>\n",
       "      <td>G</td>\n",
       "      <td>0.7141</td>\n",
       "      <td>0.7121</td>\n",
       "      <td>0.993152</td>\n",
       "      <td>1.010660</td>\n",
       "      <td>0.0138</td>\n",
       "      <td>...</td>\n",
       "      <td>6</td>\n",
       "      <td>++-+++-+-+--+++-+++++----+++-++---+++-+-+-++++...</td>\n",
       "      <td>26.7</td>\n",
       "      <td>69</td>\n",
       "      <td>0.024050</td>\n",
       "      <td>29529</td>\n",
       "      <td>166007</td>\n",
       "      <td>86058.0</td>\n",
       "      <td>2</td>\n",
       "      <td>Schizophrenia</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>13</td>\n",
       "      <td>rs6311</td>\n",
       "      <td>47471478</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>0.3938</td>\n",
       "      <td>0.3960</td>\n",
       "      <td>0.996061</td>\n",
       "      <td>0.991040</td>\n",
       "      <td>0.0127</td>\n",
       "      <td>...</td>\n",
       "      <td>29</td>\n",
       "      <td>-+++-++------+---+-+++++-+---+----++----+-+-++...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>69</td>\n",
       "      <td>0.975200</td>\n",
       "      <td>29529</td>\n",
       "      <td>166007</td>\n",
       "      <td>86058.0</td>\n",
       "      <td>13</td>\n",
       "      <td>PTSD</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>2</td>\n",
       "      <td>rs2949006</td>\n",
       "      <td>200715388</td>\n",
       "      <td>T</td>\n",
       "      <td>G</td>\n",
       "      <td>0.1803</td>\n",
       "      <td>0.1800</td>\n",
       "      <td>0.996297</td>\n",
       "      <td>0.988566</td>\n",
       "      <td>0.0166</td>\n",
       "      <td>...</td>\n",
       "      <td>6</td>\n",
       "      <td>+++-++++-+-+-------+-+--+----++++++---++--+---...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>69</td>\n",
       "      <td>0.873900</td>\n",
       "      <td>29529</td>\n",
       "      <td>166007</td>\n",
       "      <td>86058.0</td>\n",
       "      <td>2</td>\n",
       "      <td>Schizophrenia</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>10</td>\n",
       "      <td>rs7085104</td>\n",
       "      <td>104628873</td>\n",
       "      <td>A</td>\n",
       "      <td>G</td>\n",
       "      <td>0.6430</td>\n",
       "      <td>0.6406</td>\n",
       "      <td>1.001530</td>\n",
       "      <td>1.008740</td>\n",
       "      <td>0.0130</td>\n",
       "      <td>...</td>\n",
       "      <td>65</td>\n",
       "      <td>++-+-+-+---++++-+--+-+--+-+-+-+++---+-+-+-+-++...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>69</td>\n",
       "      <td>0.762100</td>\n",
       "      <td>29529</td>\n",
       "      <td>166007</td>\n",
       "      <td>86058.0</td>\n",
       "      <td>10</td>\n",
       "      <td>Schizophrenia</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>1</td>\n",
       "      <td>rs4660761</td>\n",
       "      <td>44440146</td>\n",
       "      <td>A</td>\n",
       "      <td>G</td>\n",
       "      <td>0.6703</td>\n",
       "      <td>0.6707</td>\n",
       "      <td>1.000070</td>\n",
       "      <td>0.990644</td>\n",
       "      <td>0.0160</td>\n",
       "      <td>...</td>\n",
       "      <td>26</td>\n",
       "      <td>+--+-----+++---+-+--+-+--++-++--+++++---+-+--+...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>69</td>\n",
       "      <td>0.801000</td>\n",
       "      <td>29529</td>\n",
       "      <td>166007</td>\n",
       "      <td>86058.0</td>\n",
       "      <td>1</td>\n",
       "      <td>Neurofibramatosis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>7</td>\n",
       "      <td>rs16139</td>\n",
       "      <td>24324879</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>0.9642</td>\n",
       "      <td>0.9633</td>\n",
       "      <td>0.995928</td>\n",
       "      <td>1.018770</td>\n",
       "      <td>0.0389</td>\n",
       "      <td>...</td>\n",
       "      <td>51</td>\n",
       "      <td>+-+-++--+--+++++-+--++--++++-++--+---?????????...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>52</td>\n",
       "      <td>0.839800</td>\n",
       "      <td>24132</td>\n",
       "      <td>153914</td>\n",
       "      <td>72552.2</td>\n",
       "      <td>7</td>\n",
       "      <td>PTSD</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>11</td>\n",
       "      <td>rs1801028</td>\n",
       "      <td>113283484</td>\n",
       "      <td>C</td>\n",
       "      <td>G</td>\n",
       "      <td>0.0218</td>\n",
       "      <td>0.0214</td>\n",
       "      <td>0.981607</td>\n",
       "      <td>0.981179</td>\n",
       "      <td>0.0508</td>\n",
       "      <td>...</td>\n",
       "      <td>25</td>\n",
       "      <td>++---+-++--++---+++-++--++--+++++++--?????????...</td>\n",
       "      <td>11.4</td>\n",
       "      <td>48</td>\n",
       "      <td>0.250300</td>\n",
       "      <td>25128</td>\n",
       "      <td>155015</td>\n",
       "      <td>74682.2</td>\n",
       "      <td>11</td>\n",
       "      <td>PTSD</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>6</td>\n",
       "      <td>rs3800373</td>\n",
       "      <td>35542476</td>\n",
       "      <td>A</td>\n",
       "      <td>C</td>\n",
       "      <td>0.6842</td>\n",
       "      <td>0.6822</td>\n",
       "      <td>1.002910</td>\n",
       "      <td>1.004510</td>\n",
       "      <td>0.0135</td>\n",
       "      <td>...</td>\n",
       "      <td>66</td>\n",
       "      <td>++++++-+?+--+-+-------+--+-+-++++--+-+--+-+-+-...</td>\n",
       "      <td>17.7</td>\n",
       "      <td>68</td>\n",
       "      <td>0.109900</td>\n",
       "      <td>29381</td>\n",
       "      <td>165958</td>\n",
       "      <td>85910.7</td>\n",
       "      <td>6</td>\n",
       "      <td>PTSD</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>9</td>\n",
       "      <td>rs1611115</td>\n",
       "      <td>136500515</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>0.2288</td>\n",
       "      <td>0.2298</td>\n",
       "      <td>0.971114</td>\n",
       "      <td>0.995411</td>\n",
       "      <td>0.0155</td>\n",
       "      <td>...</td>\n",
       "      <td>21</td>\n",
       "      <td>---+++-----+-++-+-++-----+--++-+-+-+++-++--+-+...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>69</td>\n",
       "      <td>0.803300</td>\n",
       "      <td>29529</td>\n",
       "      <td>166007</td>\n",
       "      <td>86058.0</td>\n",
       "      <td>9</td>\n",
       "      <td>PTSD</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20</th>\n",
       "      <td>11</td>\n",
       "      <td>rs1799732</td>\n",
       "      <td>113346251</td>\n",
       "      <td>T</td>\n",
       "      <td>TG</td>\n",
       "      <td>0.2839</td>\n",
       "      <td>0.2847</td>\n",
       "      <td>0.990769</td>\n",
       "      <td>0.996008</td>\n",
       "      <td>0.0185</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>+-+-----+-+-+--++++-++?--+---++-++++?-+---+-++...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>67</td>\n",
       "      <td>0.877300</td>\n",
       "      <td>18842</td>\n",
       "      <td>48549</td>\n",
       "      <td>46917.1</td>\n",
       "      <td>11</td>\n",
       "      <td>PTSD</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21</th>\n",
       "      <td>1</td>\n",
       "      <td>rs7161</td>\n",
       "      <td>44438974</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>0.6575</td>\n",
       "      <td>0.6569</td>\n",
       "      <td>1.002350</td>\n",
       "      <td>0.997304</td>\n",
       "      <td>0.0152</td>\n",
       "      <td>...</td>\n",
       "      <td>54</td>\n",
       "      <td>+-+-+---++-+---+-++-+-+--+++++-+-+++---++-+---...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>69</td>\n",
       "      <td>0.902800</td>\n",
       "      <td>29529</td>\n",
       "      <td>166007</td>\n",
       "      <td>86058.0</td>\n",
       "      <td>1</td>\n",
       "      <td>Neurofibromatosis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22</th>\n",
       "      <td>18</td>\n",
       "      <td>rs4801131</td>\n",
       "      <td>52752700</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>0.3894</td>\n",
       "      <td>0.3870</td>\n",
       "      <td>0.998131</td>\n",
       "      <td>0.998002</td>\n",
       "      <td>0.0127</td>\n",
       "      <td>...</td>\n",
       "      <td>6</td>\n",
       "      <td>+--+++-++++++--++---------++++-+--++--++----++...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>69</td>\n",
       "      <td>0.534600</td>\n",
       "      <td>29529</td>\n",
       "      <td>166007</td>\n",
       "      <td>86058.0</td>\n",
       "      <td>18</td>\n",
       "      <td>Schizophrenia</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>23</th>\n",
       "      <td>1</td>\n",
       "      <td>rs1198588</td>\n",
       "      <td>98552832</td>\n",
       "      <td>A</td>\n",
       "      <td>T</td>\n",
       "      <td>0.2213</td>\n",
       "      <td>0.2216</td>\n",
       "      <td>0.993490</td>\n",
       "      <td>0.997603</td>\n",
       "      <td>0.0155</td>\n",
       "      <td>...</td>\n",
       "      <td>12</td>\n",
       "      <td>--+++--++-+++---+--+----++++-++-++-++++-++-+-+...</td>\n",
       "      <td>8.4</td>\n",
       "      <td>69</td>\n",
       "      <td>0.280700</td>\n",
       "      <td>29529</td>\n",
       "      <td>166007</td>\n",
       "      <td>86058.0</td>\n",
       "      <td>1</td>\n",
       "      <td>Schizophrenia</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>24</th>\n",
       "      <td>12</td>\n",
       "      <td>rs1006737</td>\n",
       "      <td>2345295</td>\n",
       "      <td>A</td>\n",
       "      <td>G</td>\n",
       "      <td>0.3621</td>\n",
       "      <td>0.3624</td>\n",
       "      <td>0.997919</td>\n",
       "      <td>0.999600</td>\n",
       "      <td>0.0131</td>\n",
       "      <td>...</td>\n",
       "      <td>54</td>\n",
       "      <td>++++-++?+++-++-+---------++---+----++-+-++-?+-...</td>\n",
       "      <td>6.4</td>\n",
       "      <td>67</td>\n",
       "      <td>0.327800</td>\n",
       "      <td>29190</td>\n",
       "      <td>165813</td>\n",
       "      <td>85566.6</td>\n",
       "      <td>12</td>\n",
       "      <td>Schizophrenia</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>25 rows × 21 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "    CHR         SNP         BP A1  A2  FRQ_A_29529  FRQ_U_166145      INFO  \\\n",
       "0     5   rs2910032  152540354  T   C       0.5023        0.5105  0.997635   \n",
       "1     8   rs4129585  143312933  A   C       0.3996        0.3937  1.000940   \n",
       "2     3   rs4687552   52838402  T   C       0.6551        0.6497  0.997296   \n",
       "3     1     rs14403  243663893  T   C       0.1968        0.2008  0.989069   \n",
       "4    11   rs1079597  113296286  T   C       0.1989        0.1941  0.998944   \n",
       "5     8  rs11995572   89592083  T   G       0.2577        0.2559  0.996287   \n",
       "6    12  rs11532322  123731423  A   G       0.3552        0.3569  1.000640   \n",
       "7    11   rs1800497  113270828  A   G       0.2659        0.2628  0.997417   \n",
       "8     5      rs6189  142780339  T   C       0.0275        0.0274  0.997180   \n",
       "9     7   rs6461049    2017445  T   C       0.5505        0.5514  0.996514   \n",
       "10   10  rs17691888   18734528  A   G       0.1441        0.1473  0.959657   \n",
       "11    2    rs778371  233743109  A   G       0.7141        0.7121  0.993152   \n",
       "12   13      rs6311   47471478  T   C       0.3938        0.3960  0.996061   \n",
       "13    2   rs2949006  200715388  T   G       0.1803        0.1800  0.996297   \n",
       "14   10   rs7085104  104628873  A   G       0.6430        0.6406  1.001530   \n",
       "15    1   rs4660761   44440146  A   G       0.6703        0.6707  1.000070   \n",
       "16    7     rs16139   24324879  T   C       0.9642        0.9633  0.995928   \n",
       "17   11   rs1801028  113283484  C   G       0.0218        0.0214  0.981607   \n",
       "18    6   rs3800373   35542476  A   C       0.6842        0.6822  1.002910   \n",
       "19    9   rs1611115  136500515  T   C       0.2288        0.2298  0.971114   \n",
       "20   11   rs1799732  113346251  T  TG       0.2839        0.2847  0.990769   \n",
       "21    1      rs7161   44438974  T   C       0.6575        0.6569  1.002350   \n",
       "22   18   rs4801131   52752700  T   C       0.3894        0.3870  0.998131   \n",
       "23    1   rs1198588   98552832  A   T       0.2213        0.2216  0.993490   \n",
       "24   12   rs1006737    2345295  A   G       0.3621        0.3624  0.997919   \n",
       "\n",
       "          OR      SE  ...  ngt  \\\n",
       "0   0.957241  0.0127  ...   10   \n",
       "1   1.034790  0.0135  ...   68   \n",
       "2   1.030870  0.0132  ...    6   \n",
       "3   0.963965  0.0162  ...   15   \n",
       "4   1.035210  0.0164  ...   66   \n",
       "5   1.017450  0.0160  ...    1   \n",
       "6   0.985309  0.0145  ...    1   \n",
       "7   1.014610  0.0146  ...   46   \n",
       "8   1.042580  0.0444  ...   35   \n",
       "9   0.988467  0.0127  ...   63   \n",
       "10  0.982751  0.0208  ...    6   \n",
       "11  1.010660  0.0138  ...    6   \n",
       "12  0.991040  0.0127  ...   29   \n",
       "13  0.988566  0.0166  ...    6   \n",
       "14  1.008740  0.0130  ...   65   \n",
       "15  0.990644  0.0160  ...   26   \n",
       "16  1.018770  0.0389  ...   51   \n",
       "17  0.981179  0.0508  ...   25   \n",
       "18  1.004510  0.0135  ...   66   \n",
       "19  0.995411  0.0155  ...   21   \n",
       "20  0.996008  0.0185  ...    0   \n",
       "21  0.997304  0.0152  ...   54   \n",
       "22  0.998002  0.0127  ...    6   \n",
       "23  0.997603  0.0155  ...   12   \n",
       "24  0.999600  0.0131  ...   54   \n",
       "\n",
       "                                            Direction HetISqt  HetDf  \\\n",
       "0   -+-------+--+-++----++--+-+-+------+----++-+-+...    41.5     69   \n",
       "1   -+-+-+-+-+++-++++-++++--+++++--+-++++++++++++-...     4.2     69   \n",
       "2   +---+++-+++-+-+-+-+---+---+++--++++-++++--++++...     0.0     69   \n",
       "3   ---------++--++--+--+--+--++++++-------+--+--+...    11.5     69   \n",
       "4   -++---++-+-+-+++-+++-+--+--++-++-+-++++-+--+++...     0.0     69   \n",
       "5   +-+------++-+-+--+++++++----+-+-+-+-?-+-++--++...     0.0     68   \n",
       "6   ++-+++-+++-+--+---++--+++---+-++++-+-++++-+---...    17.6     69   \n",
       "7   -+++--++-+-+-+++--++-+-----++-++++-++++-+--+++...     0.0     69   \n",
       "8   ++-++---+++-+-+-+-+-+-+--+-++++--+-++??????-??...     0.0     48   \n",
       "9   --++---+-++++++++-----+--+-+++++-+----++-+-+--...     0.0     69   \n",
       "10  -+-+--+---++++-+----+-----+++-++--++?--++++++-...     6.5     68   \n",
       "11  ++-+++-+-+--+++-+++++----+++-++---+++-+-+-++++...    26.7     69   \n",
       "12  -+++-++------+---+-+++++-+---+----++----+-+-++...     0.0     69   \n",
       "13  +++-++++-+-+-------+-+--+----++++++---++--+---...     0.0     69   \n",
       "14  ++-+-+-+---++++-+--+-+--+-+-+-+++---+-+-+-+-++...     0.0     69   \n",
       "15  +--+-----+++---+-+--+-+--++-++--+++++---+-+--+...     0.0     69   \n",
       "16  +-+-++--+--+++++-+--++--++++-++--+---?????????...     0.0     52   \n",
       "17  ++---+-++--++---+++-++--++--+++++++--?????????...    11.4     48   \n",
       "18  ++++++-+?+--+-+-------+--+-+-++++--+-+--+-+-+-...    17.7     68   \n",
       "19  ---+++-----+-++-+-++-----+--++-+-+-+++-++--+-+...     0.0     69   \n",
       "20  +-+-----+-+-+--++++-++?--+---++-++++?-+---+-++...     0.0     67   \n",
       "21  +-+-+---++-+---+-++-+-+--+++++-+-+++---++-+---...     0.0     69   \n",
       "22  +--+++-++++++--++---------++++-+--++--++----++...     0.0     69   \n",
       "23  --+++--++-+++---+--+----++++-++-++-++++-++-+-+...     8.4     69   \n",
       "24  ++++-++?+++-++-+---------++---+----++-+-++-?+-...     6.4     67   \n",
       "\n",
       "      HetPVa    Nca     Nco     Neff  Chromosome       Disease_Name  \n",
       "0   0.000223  29529  166007  86058.0           5      Schizophrenia  \n",
       "1   0.377500  29529  166007  86058.0           8      Schizophrenia  \n",
       "2   0.541400  29529  166007  86058.0           3      Schizophrenia  \n",
       "3   0.215800  29529  166007  86058.0           1      Schizophrenia  \n",
       "4   0.999100  29529  166007  86058.0          11               PTSD  \n",
       "5   0.820000  19167   50346  48018.0           8      Schizophrenia  \n",
       "6   0.108500  29529  166007  86058.0          12      Schizophrenia  \n",
       "7   0.809400  29529  166007  86058.0          11               PTSD  \n",
       "8   0.720800  23581  152505  71272.5           5               PTSD  \n",
       "9   0.797500  29529  166007  86058.0           7      Schizophrenia  \n",
       "10  0.326100  19167   50346  48018.0          10      Schizophrenia  \n",
       "11  0.024050  29529  166007  86058.0           2      Schizophrenia  \n",
       "12  0.975200  29529  166007  86058.0          13               PTSD  \n",
       "13  0.873900  29529  166007  86058.0           2      Schizophrenia  \n",
       "14  0.762100  29529  166007  86058.0          10      Schizophrenia  \n",
       "15  0.801000  29529  166007  86058.0           1  Neurofibramatosis  \n",
       "16  0.839800  24132  153914  72552.2           7               PTSD  \n",
       "17  0.250300  25128  155015  74682.2          11               PTSD  \n",
       "18  0.109900  29381  165958  85910.7           6               PTSD  \n",
       "19  0.803300  29529  166007  86058.0           9               PTSD  \n",
       "20  0.877300  18842   48549  46917.1          11               PTSD  \n",
       "21  0.902800  29529  166007  86058.0           1  Neurofibromatosis  \n",
       "22  0.534600  29529  166007  86058.0          18      Schizophrenia  \n",
       "23  0.280700  29529  166007  86058.0           1      Schizophrenia  \n",
       "24  0.327800  29190  165813  85566.6          12      Schizophrenia  \n",
       "\n",
       "[25 rows x 21 columns]"
      ]
     },
     "execution_count": 26,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ptsd_data_all = ptsd_df_2.merge(all_snps, on='SNP')\n",
    "ptsd_data_all"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "id": "prepared-clock",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "0     0.000579\n",
       "1     0.011480\n",
       "2     0.021360\n",
       "3     0.023180\n",
       "4     0.034800\n",
       "5     0.277600\n",
       "6     0.306500\n",
       "7     0.321400\n",
       "8     0.347900\n",
       "9     0.362900\n",
       "10    0.401500\n",
       "11    0.444200\n",
       "12    0.480600\n",
       "13    0.490900\n",
       "14    0.501200\n",
       "15    0.554100\n",
       "16    0.632400\n",
       "17    0.708500\n",
       "18    0.738500\n",
       "19    0.767000\n",
       "20    0.829200\n",
       "21    0.859900\n",
       "22    0.876800\n",
       "23    0.878700\n",
       "24    0.975200\n",
       "Name: P, dtype: float64"
      ]
     },
     "execution_count": 27,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ptsd_data_all['P']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "id": "promising-international",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>CHR</th>\n",
       "      <th>SNP</th>\n",
       "      <th>BP</th>\n",
       "      <th>A1</th>\n",
       "      <th>A2</th>\n",
       "      <th>FRQ_A_29529</th>\n",
       "      <th>FRQ_U_166145</th>\n",
       "      <th>INFO</th>\n",
       "      <th>OR</th>\n",
       "      <th>SE</th>\n",
       "      <th>...</th>\n",
       "      <th>ngt</th>\n",
       "      <th>Direction</th>\n",
       "      <th>HetISqt</th>\n",
       "      <th>HetDf</th>\n",
       "      <th>HetPVa</th>\n",
       "      <th>Nca</th>\n",
       "      <th>Nco</th>\n",
       "      <th>Neff</th>\n",
       "      <th>Chromosome</th>\n",
       "      <th>Disease_Name</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>11</td>\n",
       "      <td>rs1079597</td>\n",
       "      <td>113296286</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>0.1989</td>\n",
       "      <td>0.1941</td>\n",
       "      <td>0.998944</td>\n",
       "      <td>1.035210</td>\n",
       "      <td>0.0164</td>\n",
       "      <td>...</td>\n",
       "      <td>66</td>\n",
       "      <td>-++---++-+-+-+++-+++-+--+--++-++-+-++++-+--+++...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>69</td>\n",
       "      <td>0.9991</td>\n",
       "      <td>29529</td>\n",
       "      <td>166007</td>\n",
       "      <td>86058.0</td>\n",
       "      <td>11</td>\n",
       "      <td>PTSD</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>11</td>\n",
       "      <td>rs1800497</td>\n",
       "      <td>113270828</td>\n",
       "      <td>A</td>\n",
       "      <td>G</td>\n",
       "      <td>0.2659</td>\n",
       "      <td>0.2628</td>\n",
       "      <td>0.997417</td>\n",
       "      <td>1.014610</td>\n",
       "      <td>0.0146</td>\n",
       "      <td>...</td>\n",
       "      <td>46</td>\n",
       "      <td>-+++--++-+-+-+++--++-+-----++-++++-++++-+--+++...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>69</td>\n",
       "      <td>0.8094</td>\n",
       "      <td>29529</td>\n",
       "      <td>166007</td>\n",
       "      <td>86058.0</td>\n",
       "      <td>11</td>\n",
       "      <td>PTSD</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>5</td>\n",
       "      <td>rs6189</td>\n",
       "      <td>142780339</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>0.0275</td>\n",
       "      <td>0.0274</td>\n",
       "      <td>0.997180</td>\n",
       "      <td>1.042580</td>\n",
       "      <td>0.0444</td>\n",
       "      <td>...</td>\n",
       "      <td>35</td>\n",
       "      <td>++-++---+++-+-+-+-+-+-+--+-++++--+-++??????-??...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>48</td>\n",
       "      <td>0.7208</td>\n",
       "      <td>23581</td>\n",
       "      <td>152505</td>\n",
       "      <td>71272.5</td>\n",
       "      <td>5</td>\n",
       "      <td>PTSD</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>13</td>\n",
       "      <td>rs6311</td>\n",
       "      <td>47471478</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>0.3938</td>\n",
       "      <td>0.3960</td>\n",
       "      <td>0.996061</td>\n",
       "      <td>0.991040</td>\n",
       "      <td>0.0127</td>\n",
       "      <td>...</td>\n",
       "      <td>29</td>\n",
       "      <td>-+++-++------+---+-+++++-+---+----++----+-+-++...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>69</td>\n",
       "      <td>0.9752</td>\n",
       "      <td>29529</td>\n",
       "      <td>166007</td>\n",
       "      <td>86058.0</td>\n",
       "      <td>13</td>\n",
       "      <td>PTSD</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>7</td>\n",
       "      <td>rs16139</td>\n",
       "      <td>24324879</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>0.9642</td>\n",
       "      <td>0.9633</td>\n",
       "      <td>0.995928</td>\n",
       "      <td>1.018770</td>\n",
       "      <td>0.0389</td>\n",
       "      <td>...</td>\n",
       "      <td>51</td>\n",
       "      <td>+-+-++--+--+++++-+--++--++++-++--+---?????????...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>52</td>\n",
       "      <td>0.8398</td>\n",
       "      <td>24132</td>\n",
       "      <td>153914</td>\n",
       "      <td>72552.2</td>\n",
       "      <td>7</td>\n",
       "      <td>PTSD</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>11</td>\n",
       "      <td>rs1801028</td>\n",
       "      <td>113283484</td>\n",
       "      <td>C</td>\n",
       "      <td>G</td>\n",
       "      <td>0.0218</td>\n",
       "      <td>0.0214</td>\n",
       "      <td>0.981607</td>\n",
       "      <td>0.981179</td>\n",
       "      <td>0.0508</td>\n",
       "      <td>...</td>\n",
       "      <td>25</td>\n",
       "      <td>++---+-++--++---+++-++--++--+++++++--?????????...</td>\n",
       "      <td>11.4</td>\n",
       "      <td>48</td>\n",
       "      <td>0.2503</td>\n",
       "      <td>25128</td>\n",
       "      <td>155015</td>\n",
       "      <td>74682.2</td>\n",
       "      <td>11</td>\n",
       "      <td>PTSD</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>6</td>\n",
       "      <td>rs3800373</td>\n",
       "      <td>35542476</td>\n",
       "      <td>A</td>\n",
       "      <td>C</td>\n",
       "      <td>0.6842</td>\n",
       "      <td>0.6822</td>\n",
       "      <td>1.002910</td>\n",
       "      <td>1.004510</td>\n",
       "      <td>0.0135</td>\n",
       "      <td>...</td>\n",
       "      <td>66</td>\n",
       "      <td>++++++-+?+--+-+-------+--+-+-++++--+-+--+-+-+-...</td>\n",
       "      <td>17.7</td>\n",
       "      <td>68</td>\n",
       "      <td>0.1099</td>\n",
       "      <td>29381</td>\n",
       "      <td>165958</td>\n",
       "      <td>85910.7</td>\n",
       "      <td>6</td>\n",
       "      <td>PTSD</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>9</td>\n",
       "      <td>rs1611115</td>\n",
       "      <td>136500515</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>0.2288</td>\n",
       "      <td>0.2298</td>\n",
       "      <td>0.971114</td>\n",
       "      <td>0.995411</td>\n",
       "      <td>0.0155</td>\n",
       "      <td>...</td>\n",
       "      <td>21</td>\n",
       "      <td>---+++-----+-++-+-++-----+--++-+-+-+++-++--+-+...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>69</td>\n",
       "      <td>0.8033</td>\n",
       "      <td>29529</td>\n",
       "      <td>166007</td>\n",
       "      <td>86058.0</td>\n",
       "      <td>9</td>\n",
       "      <td>PTSD</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>11</td>\n",
       "      <td>rs1799732</td>\n",
       "      <td>113346251</td>\n",
       "      <td>T</td>\n",
       "      <td>TG</td>\n",
       "      <td>0.2839</td>\n",
       "      <td>0.2847</td>\n",
       "      <td>0.990769</td>\n",
       "      <td>0.996008</td>\n",
       "      <td>0.0185</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>+-+-----+-+-+--++++-++?--+---++-++++?-+---+-++...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>67</td>\n",
       "      <td>0.8773</td>\n",
       "      <td>18842</td>\n",
       "      <td>48549</td>\n",
       "      <td>46917.1</td>\n",
       "      <td>11</td>\n",
       "      <td>PTSD</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>9 rows × 21 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "   CHR        SNP         BP A1  A2  FRQ_A_29529  FRQ_U_166145      INFO  \\\n",
       "0   11  rs1079597  113296286  T   C       0.1989        0.1941  0.998944   \n",
       "1   11  rs1800497  113270828  A   G       0.2659        0.2628  0.997417   \n",
       "2    5     rs6189  142780339  T   C       0.0275        0.0274  0.997180   \n",
       "3   13     rs6311   47471478  T   C       0.3938        0.3960  0.996061   \n",
       "4    7    rs16139   24324879  T   C       0.9642        0.9633  0.995928   \n",
       "5   11  rs1801028  113283484  C   G       0.0218        0.0214  0.981607   \n",
       "6    6  rs3800373   35542476  A   C       0.6842        0.6822  1.002910   \n",
       "7    9  rs1611115  136500515  T   C       0.2288        0.2298  0.971114   \n",
       "8   11  rs1799732  113346251  T  TG       0.2839        0.2847  0.990769   \n",
       "\n",
       "         OR      SE  ...  ngt  \\\n",
       "0  1.035210  0.0164  ...   66   \n",
       "1  1.014610  0.0146  ...   46   \n",
       "2  1.042580  0.0444  ...   35   \n",
       "3  0.991040  0.0127  ...   29   \n",
       "4  1.018770  0.0389  ...   51   \n",
       "5  0.981179  0.0508  ...   25   \n",
       "6  1.004510  0.0135  ...   66   \n",
       "7  0.995411  0.0155  ...   21   \n",
       "8  0.996008  0.0185  ...    0   \n",
       "\n",
       "                                           Direction HetISqt  HetDf  HetPVa  \\\n",
       "0  -++---++-+-+-+++-+++-+--+--++-++-+-++++-+--+++...     0.0     69  0.9991   \n",
       "1  -+++--++-+-+-+++--++-+-----++-++++-++++-+--+++...     0.0     69  0.8094   \n",
       "2  ++-++---+++-+-+-+-+-+-+--+-++++--+-++??????-??...     0.0     48  0.7208   \n",
       "3  -+++-++------+---+-+++++-+---+----++----+-+-++...     0.0     69  0.9752   \n",
       "4  +-+-++--+--+++++-+--++--++++-++--+---?????????...     0.0     52  0.8398   \n",
       "5  ++---+-++--++---+++-++--++--+++++++--?????????...    11.4     48  0.2503   \n",
       "6  ++++++-+?+--+-+-------+--+-+-++++--+-+--+-+-+-...    17.7     68  0.1099   \n",
       "7  ---+++-----+-++-+-++-----+--++-+-+-+++-++--+-+...     0.0     69  0.8033   \n",
       "8  +-+-----+-+-+--++++-++?--+---++-++++?-+---+-++...     0.0     67  0.8773   \n",
       "\n",
       "     Nca     Nco     Neff  Chromosome  Disease_Name  \n",
       "0  29529  166007  86058.0          11          PTSD  \n",
       "1  29529  166007  86058.0          11          PTSD  \n",
       "2  23581  152505  71272.5           5          PTSD  \n",
       "3  29529  166007  86058.0          13          PTSD  \n",
       "4  24132  153914  72552.2           7          PTSD  \n",
       "5  25128  155015  74682.2          11          PTSD  \n",
       "6  29381  165958  85910.7           6          PTSD  \n",
       "7  29529  166007  86058.0           9          PTSD  \n",
       "8  18842   48549  46917.1          11          PTSD  \n",
       "\n",
       "[9 rows x 21 columns]"
      ]
     },
     "execution_count": 28,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ptsd_data = ptsd_df_2.merge(all_snps_filt, on='SNP')\n",
    "ptsd_data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "id": "subsequent-roller",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "0    0.0348\n",
       "1    0.3214\n",
       "2    0.3479\n",
       "3    0.4806\n",
       "4    0.6324\n",
       "5    0.7085\n",
       "6    0.7385\n",
       "7    0.7670\n",
       "8    0.8292\n",
       "Name: P, dtype: float64"
      ]
     },
     "execution_count": 29,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ptsd_data['P']"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "devoted-january",
   "metadata": {},
   "source": [
    "### Performing PRS for PTSD"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "id": "alternate-person",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "      <th></th>\n",
       "      <th>Unnamed: 0</th>\n",
       "      <th>#CHROM</th>\n",
       "      <th>POS</th>\n",
       "      <th>SNP</th>\n",
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       "      <td>0.902800</td>\n",
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       "      <td>166007</td>\n",
       "      <td>86058.0</td>\n",
       "      <td>1</td>\n",
       "      <td>Neurofibromatosis</td>\n",
       "    </tr>\n",
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       "      <th>1</th>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>44440146</td>\n",
       "      <td>rs4660761</td>\n",
       "      <td>G</td>\n",
       "      <td>A</td>\n",
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       "      <td>26</td>\n",
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       "      <td>166007</td>\n",
       "      <td>86058.0</td>\n",
       "      <td>1</td>\n",
       "      <td>Neurofibramatosis</td>\n",
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       "      <td>1</td>\n",
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       "      <td>rs1198588</td>\n",
       "      <td>A</td>\n",
       "      <td>T</td>\n",
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       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
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       "      <td>12</td>\n",
       "      <td>--+++--++-+++---+--+----++++-++-++-++++-++-+-+...</td>\n",
       "      <td>8.4</td>\n",
       "      <td>69</td>\n",
       "      <td>0.280700</td>\n",
       "      <td>29529</td>\n",
       "      <td>166007</td>\n",
       "      <td>86058.0</td>\n",
       "      <td>1</td>\n",
       "      <td>Schizophrenia</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>3</td>\n",
       "      <td>1</td>\n",
       "      <td>243663893</td>\n",
       "      <td>rs14403</td>\n",
       "      <td>C</td>\n",
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       "      <td>166007</td>\n",
       "      <td>86058.0</td>\n",
       "      <td>1</td>\n",
       "      <td>Schizophrenia</td>\n",
       "    </tr>\n",
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       "      <th>4</th>\n",
       "      <td>4</td>\n",
       "      <td>2</td>\n",
       "      <td>200715388</td>\n",
       "      <td>rs2949006</td>\n",
       "      <td>T</td>\n",
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       "      <td>166007</td>\n",
       "      <td>86058.0</td>\n",
       "      <td>2</td>\n",
       "      <td>Schizophrenia</td>\n",
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       "      <td>86058.0</td>\n",
       "      <td>2</td>\n",
       "      <td>Schizophrenia</td>\n",
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       "      <td>29529</td>\n",
       "      <td>166007</td>\n",
       "      <td>86058.0</td>\n",
       "      <td>3</td>\n",
       "      <td>Schizophrenia</td>\n",
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       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>7</td>\n",
       "      <td>5</td>\n",
       "      <td>142780339</td>\n",
       "      <td>rs6189</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
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       "      <td>35</td>\n",
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       "      <td>23581</td>\n",
       "      <td>152505</td>\n",
       "      <td>71272.5</td>\n",
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       "      <td>PTSD</td>\n",
       "    </tr>\n",
       "    <tr>\n",
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       "      <td>166007</td>\n",
       "      <td>86058.0</td>\n",
       "      <td>5</td>\n",
       "      <td>Schizophrenia</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>9</td>\n",
       "      <td>6</td>\n",
       "      <td>35542476</td>\n",
       "      <td>rs3800373</td>\n",
       "      <td>C</td>\n",
       "      <td>A</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>...</td>\n",
       "      <td>66</td>\n",
       "      <td>++++++-+?+--+-+-------+--+-+-++++--+-+--+-+-+-...</td>\n",
       "      <td>17.7</td>\n",
       "      <td>68</td>\n",
       "      <td>0.109900</td>\n",
       "      <td>29381</td>\n",
       "      <td>165958</td>\n",
       "      <td>85910.7</td>\n",
       "      <td>6</td>\n",
       "      <td>PTSD</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>10</td>\n",
       "      <td>7</td>\n",
       "      <td>2017445</td>\n",
       "      <td>rs6461049</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>...</td>\n",
       "      <td>63</td>\n",
       "      <td>--++---+-++++++++-----+--+-+++++-+----++-+-+--...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>69</td>\n",
       "      <td>0.797500</td>\n",
       "      <td>29529</td>\n",
       "      <td>166007</td>\n",
       "      <td>86058.0</td>\n",
       "      <td>7</td>\n",
       "      <td>Schizophrenia</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>11</td>\n",
       "      <td>7</td>\n",
       "      <td>24324879</td>\n",
       "      <td>rs16139</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>51</td>\n",
       "      <td>+-+-++--+--+++++-+--++--++++-++--+---?????????...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>52</td>\n",
       "      <td>0.839800</td>\n",
       "      <td>24132</td>\n",
       "      <td>153914</td>\n",
       "      <td>72552.2</td>\n",
       "      <td>7</td>\n",
       "      <td>PTSD</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>12</td>\n",
       "      <td>8</td>\n",
       "      <td>89592083</td>\n",
       "      <td>rs11995572</td>\n",
       "      <td>G</td>\n",
       "      <td>T</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>1</td>\n",
       "      <td>+-+------++-+-+--+++++++----+-+-+-+-?-+-++--++...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>68</td>\n",
       "      <td>0.820000</td>\n",
       "      <td>19167</td>\n",
       "      <td>50346</td>\n",
       "      <td>48018.0</td>\n",
       "      <td>8</td>\n",
       "      <td>Schizophrenia</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>13</td>\n",
       "      <td>8</td>\n",
       "      <td>143312933</td>\n",
       "      <td>rs4129585</td>\n",
       "      <td>A</td>\n",
       "      <td>C</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>...</td>\n",
       "      <td>68</td>\n",
       "      <td>-+-+-+-+-+++-++++-++++--+++++--+-++++++++++++-...</td>\n",
       "      <td>4.2</td>\n",
       "      <td>69</td>\n",
       "      <td>0.377500</td>\n",
       "      <td>29529</td>\n",
       "      <td>166007</td>\n",
       "      <td>86058.0</td>\n",
       "      <td>8</td>\n",
       "      <td>Schizophrenia</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>14</td>\n",
       "      <td>9</td>\n",
       "      <td>136500515</td>\n",
       "      <td>rs1611115</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>21</td>\n",
       "      <td>---+++-----+-++-+-++-----+--++-+-+-+++-++--+-+...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>69</td>\n",
       "      <td>0.803300</td>\n",
       "      <td>29529</td>\n",
       "      <td>166007</td>\n",
       "      <td>86058.0</td>\n",
       "      <td>9</td>\n",
       "      <td>PTSD</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>15</td>\n",
       "      <td>10</td>\n",
       "      <td>18734528</td>\n",
       "      <td>rs17691888</td>\n",
       "      <td>G</td>\n",
       "      <td>A</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>6</td>\n",
       "      <td>-+-+--+---++++-+----+-----+++-++--++?--++++++-...</td>\n",
       "      <td>6.5</td>\n",
       "      <td>68</td>\n",
       "      <td>0.326100</td>\n",
       "      <td>19167</td>\n",
       "      <td>50346</td>\n",
       "      <td>48018.0</td>\n",
       "      <td>10</td>\n",
       "      <td>Schizophrenia</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>16</td>\n",
       "      <td>10</td>\n",
       "      <td>104628873</td>\n",
       "      <td>rs7085104</td>\n",
       "      <td>A</td>\n",
       "      <td>G</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>...</td>\n",
       "      <td>65</td>\n",
       "      <td>++-+-+-+---++++-+--+-+--+-+-+-+++---+-+-+-+-++...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>69</td>\n",
       "      <td>0.762100</td>\n",
       "      <td>29529</td>\n",
       "      <td>166007</td>\n",
       "      <td>86058.0</td>\n",
       "      <td>10</td>\n",
       "      <td>Schizophrenia</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>17</td>\n",
       "      <td>11</td>\n",
       "      <td>113270828</td>\n",
       "      <td>rs1800497</td>\n",
       "      <td>G</td>\n",
       "      <td>A</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>...</td>\n",
       "      <td>46</td>\n",
       "      <td>-+++--++-+-+-+++--++-+-----++-++++-++++-+--+++...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>69</td>\n",
       "      <td>0.809400</td>\n",
       "      <td>29529</td>\n",
       "      <td>166007</td>\n",
       "      <td>86058.0</td>\n",
       "      <td>11</td>\n",
       "      <td>PTSD</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>18</td>\n",
       "      <td>11</td>\n",
       "      <td>113283484</td>\n",
       "      <td>rs1801028</td>\n",
       "      <td>G</td>\n",
       "      <td>C</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>25</td>\n",
       "      <td>++---+-++--++---+++-++--++--+++++++--?????????...</td>\n",
       "      <td>11.4</td>\n",
       "      <td>48</td>\n",
       "      <td>0.250300</td>\n",
       "      <td>25128</td>\n",
       "      <td>155015</td>\n",
       "      <td>74682.2</td>\n",
       "      <td>11</td>\n",
       "      <td>PTSD</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>19</td>\n",
       "      <td>11</td>\n",
       "      <td>113296286</td>\n",
       "      <td>rs1079597</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>66</td>\n",
       "      <td>-++---++-+-+-+++-+++-+--+--++-++-+-++++-+--+++...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>69</td>\n",
       "      <td>0.999100</td>\n",
       "      <td>29529</td>\n",
       "      <td>166007</td>\n",
       "      <td>86058.0</td>\n",
       "      <td>11</td>\n",
       "      <td>PTSD</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20</th>\n",
       "      <td>20</td>\n",
       "      <td>11</td>\n",
       "      <td>113346251</td>\n",
       "      <td>rs1799732</td>\n",
       "      <td>T</td>\n",
       "      <td>TG</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>+-+-----+-+-+--++++-++?--+---++-++++?-+---+-++...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>67</td>\n",
       "      <td>0.877300</td>\n",
       "      <td>18842</td>\n",
       "      <td>48549</td>\n",
       "      <td>46917.1</td>\n",
       "      <td>11</td>\n",
       "      <td>PTSD</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21</th>\n",
       "      <td>21</td>\n",
       "      <td>12</td>\n",
       "      <td>2345295</td>\n",
       "      <td>rs1006737</td>\n",
       "      <td>G</td>\n",
       "      <td>A</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>54</td>\n",
       "      <td>++++-++?+++-++-+---------++---+----++-+-++-?+-...</td>\n",
       "      <td>6.4</td>\n",
       "      <td>67</td>\n",
       "      <td>0.327800</td>\n",
       "      <td>29190</td>\n",
       "      <td>165813</td>\n",
       "      <td>85566.6</td>\n",
       "      <td>12</td>\n",
       "      <td>Schizophrenia</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22</th>\n",
       "      <td>22</td>\n",
       "      <td>12</td>\n",
       "      <td>123731423</td>\n",
       "      <td>rs11532322</td>\n",
       "      <td>A</td>\n",
       "      <td>G</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>1</td>\n",
       "      <td>++-+++-+++-+--+---++--+++---+-++++-+-++++-+---...</td>\n",
       "      <td>17.6</td>\n",
       "      <td>69</td>\n",
       "      <td>0.108500</td>\n",
       "      <td>29529</td>\n",
       "      <td>166007</td>\n",
       "      <td>86058.0</td>\n",
       "      <td>12</td>\n",
       "      <td>Schizophrenia</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>23</th>\n",
       "      <td>23</td>\n",
       "      <td>13</td>\n",
       "      <td>47471478</td>\n",
       "      <td>rs6311</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>29</td>\n",
       "      <td>-+++-++------+---+-+++++-+---+----++----+-+-++...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>69</td>\n",
       "      <td>0.975200</td>\n",
       "      <td>29529</td>\n",
       "      <td>166007</td>\n",
       "      <td>86058.0</td>\n",
       "      <td>13</td>\n",
       "      <td>PTSD</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>24</th>\n",
       "      <td>26</td>\n",
       "      <td>18</td>\n",
       "      <td>52752700</td>\n",
       "      <td>rs4801131</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>...</td>\n",
       "      <td>6</td>\n",
       "      <td>+--+++-++++++--++---------++++-+--++--++----++...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>69</td>\n",
       "      <td>0.534600</td>\n",
       "      <td>29529</td>\n",
       "      <td>166007</td>\n",
       "      <td>86058.0</td>\n",
       "      <td>18</td>\n",
       "      <td>Schizophrenia</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>25 rows × 2530 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "    Unnamed: 0  #CHROM        POS         SNP REF ALT  HG00096  HG00097  \\\n",
       "0            0       1   44438974      rs7161   C   T        2        2   \n",
       "1            1       1   44440146   rs4660761   G   A        2        2   \n",
       "2            2       1   98552832   rs1198588   A   T        1        0   \n",
       "3            3       1  243663893     rs14403   C   T        0        0   \n",
       "4            4       2  200715388   rs2949006   T   G        2        1   \n",
       "5            5       2  233743109    rs778371   A   G        0        0   \n",
       "6            6       3   52838402   rs4687552   T   C        0        0   \n",
       "7            7       5  142780339      rs6189   C   T        0        0   \n",
       "8            8       5  152540354   rs2910032   C   T        0        1   \n",
       "9            9       6   35542476   rs3800373   C   A        1        1   \n",
       "10          10       7    2017445   rs6461049   C   T        0        1   \n",
       "11          11       7   24324879     rs16139   T   C        0        0   \n",
       "12          12       8   89592083  rs11995572   G   T        1        0   \n",
       "13          13       8  143312933   rs4129585   A   C        1        2   \n",
       "14          14       9  136500515   rs1611115   T   C        2        2   \n",
       "15          15      10   18734528  rs17691888   G   A        0        1   \n",
       "16          16      10  104628873   rs7085104   A   G        0        1   \n",
       "17          17      11  113270828   rs1800497   G   A        0        0   \n",
       "18          18      11  113283484   rs1801028   G   C        0        0   \n",
       "19          19      11  113296286   rs1079597   C   T        0        0   \n",
       "20          20      11  113346251   rs1799732   T  TG        2        2   \n",
       "21          21      12    2345295   rs1006737   G   A        1        2   \n",
       "22          22      12  123731423  rs11532322   A   G        1        2   \n",
       "23          23      13   47471478      rs6311   C   T        2        2   \n",
       "24          26      18   52752700   rs4801131   C   T        2        1   \n",
       "\n",
       "    HG00099  HG00100  ...  ngt  \\\n",
       "0         1        2  ...   54   \n",
       "1         1        2  ...   26   \n",
       "2         1        2  ...   12   \n",
       "3         1        0  ...   15   \n",
       "4         2        2  ...    6   \n",
       "5         0        0  ...    6   \n",
       "6         0        0  ...    6   \n",
       "7         0        0  ...   35   \n",
       "8         1        0  ...   10   \n",
       "9         0        2  ...   66   \n",
       "10        1        2  ...   63   \n",
       "11        0        0  ...   51   \n",
       "12        0        0  ...    1   \n",
       "13        1        1  ...   68   \n",
       "14        1        0  ...   21   \n",
       "15        0        0  ...    6   \n",
       "16        1        1  ...   65   \n",
       "17        0        1  ...   46   \n",
       "18        0        0  ...   25   \n",
       "19        0        0  ...   66   \n",
       "20        2        1  ...    0   \n",
       "21        1        0  ...   54   \n",
       "22        2        0  ...    1   \n",
       "23        1        0  ...   29   \n",
       "24        1        1  ...    6   \n",
       "\n",
       "                                            Direction  HetISqt  HetDf  \\\n",
       "0   +-+-+---++-+---+-++-+-+--+++++-+-+++---++-+---...      0.0     69   \n",
       "1   +--+-----+++---+-+--+-+--++-++--+++++---+-+--+...      0.0     69   \n",
       "2   --+++--++-+++---+--+----++++-++-++-++++-++-+-+...      8.4     69   \n",
       "3   ---------++--++--+--+--+--++++++-------+--+--+...     11.5     69   \n",
       "4   +++-++++-+-+-------+-+--+----++++++---++--+---...      0.0     69   \n",
       "5   ++-+++-+-+--+++-+++++----+++-++---+++-+-+-++++...     26.7     69   \n",
       "6   +---+++-+++-+-+-+-+---+---+++--++++-++++--++++...      0.0     69   \n",
       "7   ++-++---+++-+-+-+-+-+-+--+-++++--+-++??????-??...      0.0     48   \n",
       "8   -+-------+--+-++----++--+-+-+------+----++-+-+...     41.5     69   \n",
       "9   ++++++-+?+--+-+-------+--+-+-++++--+-+--+-+-+-...     17.7     68   \n",
       "10  --++---+-++++++++-----+--+-+++++-+----++-+-+--...      0.0     69   \n",
       "11  +-+-++--+--+++++-+--++--++++-++--+---?????????...      0.0     52   \n",
       "12  +-+------++-+-+--+++++++----+-+-+-+-?-+-++--++...      0.0     68   \n",
       "13  -+-+-+-+-+++-++++-++++--+++++--+-++++++++++++-...      4.2     69   \n",
       "14  ---+++-----+-++-+-++-----+--++-+-+-+++-++--+-+...      0.0     69   \n",
       "15  -+-+--+---++++-+----+-----+++-++--++?--++++++-...      6.5     68   \n",
       "16  ++-+-+-+---++++-+--+-+--+-+-+-+++---+-+-+-+-++...      0.0     69   \n",
       "17  -+++--++-+-+-+++--++-+-----++-++++-++++-+--+++...      0.0     69   \n",
       "18  ++---+-++--++---+++-++--++--+++++++--?????????...     11.4     48   \n",
       "19  -++---++-+-+-+++-+++-+--+--++-++-+-++++-+--+++...      0.0     69   \n",
       "20  +-+-----+-+-+--++++-++?--+---++-++++?-+---+-++...      0.0     67   \n",
       "21  ++++-++?+++-++-+---------++---+----++-+-++-?+-...      6.4     67   \n",
       "22  ++-+++-+++-+--+---++--+++---+-++++-+-++++-+---...     17.6     69   \n",
       "23  -+++-++------+---+-+++++-+---+----++----+-+-++...      0.0     69   \n",
       "24  +--+++-++++++--++---------++++-+--++--++----++...      0.0     69   \n",
       "\n",
       "      HetPVa    Nca     Nco     Neff  Chromosome       Disease_Name  \n",
       "0   0.902800  29529  166007  86058.0           1  Neurofibromatosis  \n",
       "1   0.801000  29529  166007  86058.0           1  Neurofibramatosis  \n",
       "2   0.280700  29529  166007  86058.0           1      Schizophrenia  \n",
       "3   0.215800  29529  166007  86058.0           1      Schizophrenia  \n",
       "4   0.873900  29529  166007  86058.0           2      Schizophrenia  \n",
       "5   0.024050  29529  166007  86058.0           2      Schizophrenia  \n",
       "6   0.541400  29529  166007  86058.0           3      Schizophrenia  \n",
       "7   0.720800  23581  152505  71272.5           5               PTSD  \n",
       "8   0.000223  29529  166007  86058.0           5      Schizophrenia  \n",
       "9   0.109900  29381  165958  85910.7           6               PTSD  \n",
       "10  0.797500  29529  166007  86058.0           7      Schizophrenia  \n",
       "11  0.839800  24132  153914  72552.2           7               PTSD  \n",
       "12  0.820000  19167   50346  48018.0           8      Schizophrenia  \n",
       "13  0.377500  29529  166007  86058.0           8      Schizophrenia  \n",
       "14  0.803300  29529  166007  86058.0           9               PTSD  \n",
       "15  0.326100  19167   50346  48018.0          10      Schizophrenia  \n",
       "16  0.762100  29529  166007  86058.0          10      Schizophrenia  \n",
       "17  0.809400  29529  166007  86058.0          11               PTSD  \n",
       "18  0.250300  25128  155015  74682.2          11               PTSD  \n",
       "19  0.999100  29529  166007  86058.0          11               PTSD  \n",
       "20  0.877300  18842   48549  46917.1          11               PTSD  \n",
       "21  0.327800  29190  165813  85566.6          12      Schizophrenia  \n",
       "22  0.108500  29529  166007  86058.0          12      Schizophrenia  \n",
       "23  0.975200  29529  166007  86058.0          13               PTSD  \n",
       "24  0.534600  29529  166007  86058.0          18      Schizophrenia  \n",
       "\n",
       "[25 rows x 2530 columns]"
      ]
     },
     "execution_count": 30,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ptsd_prs = simulated_off.merge(ptsd_data, on='SNP')\n",
    "ptsd_prs_2 = simulated_off.merge(ptsd_data_all, on='SNP')\n",
    "ptsd_prs_2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 33,
   "id": "cloudy-vertex",
   "metadata": {},
   "outputs": [],
   "source": [
    "column_names = simulated_off.columns.to_list()\n",
    "column_names = column_names[6:]\n",
    "column_names\n",
    "prs_individuals = []\n",
    "\n",
    "for individual in column_names:\n",
    "    ptsd_prs_2['Score'] = ptsd_prs_2.apply(lambda x: x[individual] * x['OR'], axis=1)\n",
    "    score = ptsd_prs_2['Score'].sum()\n",
    "    list_item = [individual, score]\n",
    "    prs_individuals.append(list_item)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 34,
   "id": "artistic-instruction",
   "metadata": {},
   "outputs": [],
   "source": [
    "prs_ind_df = pd.DataFrame(prs_individuals, columns=['Individuals', 'Scores'])\n",
    "prs_ind_df.to_csv('final_prs_ptsd_all_parents.csv', encoding='utf-8')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "satellite-helping",
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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