index.Rmd

--- 
site: bookdown::bookdown_site
documentclass: book
bibliography: [book.bib]
biblio-style: apalike
link-citations: yes
description: "This is wiki aims at gathering and building knowledge about best practices for genetic analyses, particularly of the iPSYCH data."
github-repo: "ipsych-community/wiki-genetics"
url: 'https\://ipsych-community.github.io/wiki-genetics/'
favicon: "images/ipsych_small.png"
---

```{r setup, include=FALSE}
# Global {knitr} options
source("knitr-options.R")
knitr::opts_chunk$set()
# Spelling check
WORDS_TO_IGNORE <- c("ShareAlike")
source("spelling-check.R")
```

# (PART) Introduction {-}

# Welcome to the iPSYCH community wiki! {-}

This wiki aims at gathering and building knowledge about best practices for genetic analyses, particularly of the iPSYCH data.

Learn more about iPSYCH there: https://ipsych.dk/en/.

Remember that this is a public space, make sure not to disclose any information that would breach ethics approvals of the data.

## How to contribute? {-}

- Small (but useful!) contributions: 

    - **opening an issue about some missing/unclear information**; whenever you have to search for some question or someone ask you a question about genetic analyses or/and iPSYCH data, please open an issue here to document that this piece of information is missing to this wiki
    
    - **participating in topic discussions** (in issues), e.g. mentioning missing information, useful references or external links
    
    - **clarifying a point in a wiki page** by adding a few sentences
    
    - **correcting typos**

- Larger contributions: 

    - **making wiki pages**
    
    - **reviewing wiki pages** (including code), by someone who is *not* expert in the corresponding topic


## Guidelines {-}

- be nice with others and welcoming to new contributors

- always open a new issue when you think about missing information (it does *not* have to be you that add the missing information afterwards)

- each page should have is own corresponding issue

- split the issues and pages as much as possible, e.g. making a GWAS using PLINK and making a GWAS using BOLT are two different issues and pages

- for complex analyses (all main ones basically), it would be good to work within teams (of e.g. two people)

## Contributing new pages {-}

See the [new file example](https://github.com/ipsych-community/wiki-genetics/blob/master/example.Rmd).

At the beginning of each R Markdown file, we should have the following code block to include both chunk options and spelling check.

````markdown
`r ''````{r setup, include=FALSE}
# Global {knitr} options
source("knitr-options.R")
knitr::opts_chunk$set()
# Spelling check
WORDS_TO_IGNORE <- c()
source("spelling-check.R")
```
````

Each new page should go into its own new R Markdown file.
You should add this new file to the (ordered) list of files to render in `rmd_files:` in file `_booldown.yml`.
The title of this new file should be an header  (`#`) and sections should have header 2 (`##`).
Include the `(PART)` section header only if this new page is the first one of a new part (collection of pages).

To preview your page locally in RStudio, you can use `Ctrl + Shift + K` (equivalent to running `bookdown::render_book("example.Rmd", encoding = 'UTF-8')`, where `example.Rmd` is the page you want to render). 
To build the entire book, which is useful to e.g. rebuild the table of content (ToC) for all pages, you can use `Ctrl + Shift + B` (equivalent to running `rmarkdown::render_site(encoding = 'UTF-8')`). 
**Before rebuilding the entire book**, you should make sure you have the latest changes locally to avoid merge conflicts.

## License {-}

This material is licensed under the [Creative Commons Attribution-ShareAlike 3.0 License](http://creativecommons.org/licenses/by-sa/3.0/).