# 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