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| author | Muriithi Frederick Muriuki | 2021-08-30 05:23:22 +0300 |
|---|---|---|
| committer | Muriithi Frederick Muriuki | 2021-08-30 05:23:22 +0300 |
| commit | c045122908d36bba4ca197f3f67e89d80958f38f (patch) | |
| tree | a415e2c30144a9934d8ccb784d858c73ac0a6caa /README.md | |
| parent | a9fa309f4017d84cd30f6df90376042f20b1836b (diff) | |
| download | genenetwork3-c045122908d36bba4ca197f3f67e89d80958f38f.tar.gz | |
Document acquired knowledge on `rust-qtlreaper`
Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/heatmaps/heatmaps.py: document format of the traits file
To assist future developers, and development of the system, this commit
documents some of the hard-won knowledge about the operation of the system
to ease future development of the system.
The documentation, if good, might also help with future onboarding of new
developers to the system.
Diffstat (limited to 'README.md')
| -rw-r--r-- | README.md | 21 |
1 files changed, 21 insertions, 0 deletions
@@ -120,3 +120,24 @@ guix. To freeze dependencies: pip freeze --path venv/lib/python3.8/site-packages > requirements.txt ``` + +## QTLReaper (rust-qtlreaper) and Trait Files + +To run QTL computations, this system makes use of the [rust-qtlreaper](https://github.com/chfi/rust-qtlreaper.git) utility. + +To do this, the system needs to export the trait data into a tab-separated file, that can then be passed to the utility using the `--traits` option. For more information about the available options, please [see the rust-qtlreaper](https://github.com/chfi/rust-qtlreaper.git) repository. + +### Traits File Format + +The traits file begins with a header row/line with the column headers. The first column in the file has the header **"Trait"**. Every other column has a header for one of the strains in consideration. + +Under the **"Trait"** column, the traits are numbered from **T1** to **T<n>** where **<n>** is the count of the total number of traits in consideration. + +As an example, you could end up with a trait file like the following: + +```txt +Traits BXD27 BXD32 DBA/2J BXD21 ... +T1 10.5735 9.27408 9.48255 9.18253 ... +T2 6.4471 6.7191 5.98015 6.68051 ... +... +``` |