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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:

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:

{
    "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:

Rscript rqtl2_wrapper.R --input_file [file_path] --directory [workspace_dir] --output_file [file_path] --nperm 100 --cores 3

Related issues:

https://issues.genenetwork.org/topics/lmms/rqtl2/using-rqtl2

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