setupGSEArun: Sets up and runs GSEA using population-based FST values

In BaderLab/POPPATHR: Population-based pathway analysis of SNP-SNP coevolution

Description

Sets up and runs GSEA using population-based FST values

Usage

setupGSEArun(
  fst_file,
  annotation_file,
  snp2gene_file,
  SET_PERM = 10000,
  SNP2GENE_DIST = 5e+05,
  MIN_GENE = 10,
  MAX_GENE = 300,
  SET_SEED = 42,
  output_folder
)

Arguments

fst_file	(char) path to file with SNP-level FST statistics.
annotation_file	(char) path to pathway definitions GMT file.
snp2gene_file	(char) path to file with snp2gene mappings (output of SNP2gene.R).
SET_PERM	(integer) set cycle of permutations to run (default=10000).
SNP2GENE_DIST	(integer) value for GSEA –distance. Max. distance between SNP and gene for their association in snp2gene_file (default=500000).
MIN_GENE	(integer) value for GSEA –setmin. Min. number of genes in a gene set to be considered (default=10).
MAX_GENE	(integer) value for GSEA –setmax. Max. number of genes in a gene set to be considered (default=300).
SET_SEED	(integer) value for GSEA –seed.
output_folder	(char) path to store output files.

Value

none

BaderLab/POPPATHR documentation built on Dec. 17, 2021, 9:53 a.m.