Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Convert blank cells to NA for consistency? #42

Open
ivelsko opened this issue Sep 15, 2021 · 0 comments
Open

Convert blank cells to NA for consistency? #42

ivelsko opened this issue Sep 15, 2021 · 0 comments

Comments

@ivelsko
Copy link

ivelsko commented Sep 15, 2021

Hi guys, I encountered some inconsistent sidora table formatting that caused me some confusion while trying to filter and join tables. In some columns where there's no entry a cell is left blank, while in others it's filled with NA. For example

df_list <- get_df_list(c(
  "TAB_Library", "TAB_Capture", "TAB_Sequencing"
), con = con)

lib_info <- join_pandora_tables(df_list)

lib_info <- convert_all_ids_to_values(lib_info, con)

lib_info %>% 
  filter(str_detect(library.Full_Library_Id, "CMC040")) %>%
  select(library.Full_Library_Id, library.Protocol, library.Batch, sequencing.Full_Sequencing_Id) 

# A tibble: 3 × 4
  library.Full_Library_Id library.Protocol       library.Batch        sequencing.Full_Sequencing_Id
  <chr>                   <chr>                  <chr>                <chr>                        
1 CMC040.A0201            dsLibrary non UDG 2015 ""                   NA                           
2 CMC040.B0101            dsLibrary non UDG 2015 "Li04_VE_2019-04-17" CMC040.B0101.SG1.1           
3 CMC040.B0101            dsLibrary non UDG 2015 "Li04_VE_2019-04-17" CMC040.B0101.SG1.2           

In Pandora the cell for the library batch is empty. Is this just an R/Pandora thing that has to be tolerated, or would it be possible to have this made consistent (everything is NA)?

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant