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.

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

```{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.