Gene Hunter based on Gene-Level Association (GH-GLA)

A R-package for gene-based association study

on Linux 2024.7.12

install

Need to install in advance: data.table, stringr, dplyr
You can install GHGLA:

install.packages("devtools")
devtools::install_github("gaze-abyss/GH-GLA")

input data

The vcf files need to be converted using vcftools:

vcftools --gzvcf yourname.vcf.gz --012 --out yourname

The phenotype data must be in csv format(There can be multiple phenotypes in this csv, each phenotype is a separate column), and a gene interval file that requires a special processing.
Phenotype data for the control group are also required.
Model3 requires SnpEff results, and refer to the examples in the /data for specific requirements.

java -jar snpEff wheat yourname.chr2D.vcf.gz > yourname.snpEff.vcf

usage

You can choose to use gla_model2 or gla_model3(Model1 is test model, not available).

rm(list=ls())
library(GHGLA)
gla_model3("chr2D",                                   #Some species' genomes are so large that they can only be counted in terms of chromosomes
            2,                                        #Which column of phenotype data is used
            "/path/data.gene.list",                   #gene interval file
            "/path/chr2D.anno.txt",                   #SnpEff results
            "/path/control_group_phenotype.csv",      #Phenotype data for the control group
            "/path/vcftoolsres/yourname",             #vcftools results
            "/path/phenotype.csv",                    #phenotype data
            "/output_path/")

about GH-GLA

It is currently in beta and the features are not complete