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# Implementation of QTL Analysis Using r-qtl2 in GeneNetwork
## Tags
* Assigned: alexm
* Keywords: RQTL, GeneNetwork2, implementation
* Type: Feature
* Status: In Progress
## Description
This document outlines the implementation of a QTL analysis tool in GeneNetwork using r-qtl2 (see docs: https://kbroman.org/qtl2/) and explains what the script does.
This PR contains the implementation of the r-qtl2 script for genenetwork:
=> https://github.com/genenetwork/genenetwork3/pull/201
## Tasks
The script currently aims to achieve the following:
* [x] Parsing arguments required for the script
* [x] Data validation for the script
* [x] Generating the cross file
* [x] Reading the cross file
* [x] Calculating genotype probabilities
* [x] Performing Geno Scan (scan1) using HK, LOCO, etc.
* [x] Finding LOD peaks
* [x] Performing permutation tests
* [x] Conducting QTL analysis for multiparent populations
* [ ] Generating required plots
## How to Run the Script
The script requires an input file containing all the necessary data to generate the control file. Example:
```json
{
"crosstype": "riself",
"geno_file": "grav2_geno.csv",
"geno_map_file": "grav2_gmap.csv",
"pheno_file": "grav2_pheno.csv",
"phenocovar_file": "grav2_phenocovar.csv"
}
```
In addition other parameters required are
* output file (A file path of where the output for the script will be generated)
* --directory ( A workspace of where to generate the control file)
Optional parameters include
* --output_file: The file path where the output for the script will be generated.
* --directory: The workspace directory where the control file will be generated.
Optional parameters:
* --cores: The number of cores to use (set to 0 for using all cores).
* --method: The scanning method to use (e.g., Haley-Knott, Linear Mixed Model, or LMM with Leave-One-Chromosome-Out).
* --pstrata: Use permutation strata.
* --threshold: Minimum LOD score for a peak.
An example of how to run the script:
```sh
Rscript rqtl2_wrapper.R --input_file [file_path] --directory [workspace_dir] --output_file [file_path] --nperm 100 --cores 3
```
## Related issues:
=> ./using/rqtl2.gmi
=> ./gn-rqtl-design-implementation.gmi
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