Description

The iRIGS (integrative risk gene selector) is a framework to identify risk genes from GWAS loci.

installation

First install the dependent package in R

library("devtools")
install_github("crotoc/iRIGS")

Second copy the binary iRIGS to your PATH

The binary iRIGS in this repository is the command to run iRIGS

Quick start

Download resource file

To run iRIGS, at least we need:

--cand_loci: Specify a candidate loci list --network: A precomputed network files saved in RData. --gene_symbol: A file including the start and end of all genes. --generic_evi_file: formated features. Will use in burnin round. --extra_evi_file: formated features. Will use in after-burnin round.

All the files used in our study can be downloaded here:

https://vanderbilt365-my.sharepoint.com/:f:/g/personal/rui_chen_1_vanderbilt_edu/EmTLMwVI5DxLtN0dz8ITJJoBeBAwk7Yw6f6vyTE36N85Mg?e=RTWEOa

Installed required R package

echo "install.packages(\"BiocManager\");library(BiocManager);BiocManager::install(c("\pacman\",\"optparse\",\"RLT\",\"data.table\",\"GenomicRanges\",\"doParallel\",\"e1071\",\"RLT\",\"stringi\",\"roxygen2\",\"devtools\"));library(devtools);install_github(\"crotoc/iRIGS\")" | R --no-save

network only mode

Gibbs --cand_loci scz.145.sub.1e-6.5e5.bed.fmt \
	  --network go_propogation_probality_rp_0.3.RData \
	  --gene_symbol 53934_transcribed_genes_GencodeV12_with_official_symbol \
	  --threads 20 \
	  --res_prefix output \
	  --res_path gibbs_result \
	  --distance TRUE \
	  --burnin_round 1000\
	  --after_burnin_round 1000 \
	  --max_gene 20 \
	  --evaluate_region FALSE \
	  --window_size 1e6

feature integrating mode

Gibbs --cand_loci scz.145.sub.1e-6.5e5.bed.fmt \
	  --network go_propogation_probality_rp_0.3.RData \
	  --gene_symbol 53934_transcribed_genes_GencodeV12_with_official_symbol \
      --generic_evi_file generic.evi \
	  --extra_evi_file generic.evi \
	  --threads 20 \
	  --res_prefix output \
	  --res_path gibbs_result \
	  --distance TRUE \
	  --burnin_round 1000 \
	  --after_burnin_round 1000 \
	  --max_gene 20 \
	  --evaluate_region FALSE \
	  --window_size 1e6

Singularity image to run iRIGS

Required sif and img

iRIGS.img: The overlay containing R and required packages. The R and packages are installed using conda. The conda ENV is located in /mylib/condaEnv/default. When invoking singularity run, this conda ENV will be loaded automatically.

BASE.sif: Singularity image containning conda ENV.

singularity run -e --bind /fs0 --overlay iRIGS.img BASE.sif iRIGS --cand_loci scz.145.sub.1e-6.5e5.bed.fmt --network go_propogation_probality_rp_0.3.RData --gene_symbol 53934_transcribed_genes_GencodeV12_with_official_symbol --generic_evi_file generic.evi --extra_evi_file generic.evi --threads 40 --res_prefix output --res_path gibbs_result --distance TRUE --burnin_round 20 --after_burnin_round 20 --max_gene 20 --window_size 1000000