writePathFiles: Generates SNP lists per selection-enriched and unenriched...

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

Description

Generates SNP lists per selection-enriched and unenriched pathway as determined by GSEA

Usage

writePathFiles(
  genotype_file,
  results_file,
  gseaStat_file,
  snp2gene_file,
  fam_file,
  EM_group_file,
  ENRICH_NES = 3,
  UNENRICH_NES = 0.1,
  enrich_folder,
  enrichEM_folder,
  unenrich_folder
)

Arguments

genotype_file	(char) path to file with SNP genotype data (PLINK format).
results_file	(char) path to files with GSEA results. Strutured to compare results of two population analyses i.e., CEU vs. YRI and CEU vs. LWK.
gseaStat_file	(char) path to GSEA statistics file.
snp2gene_file	(char) path to SNP-gene mapping file.
fam_file	(char) path to PLINK population coded fam file.
EM_group_file	(char) file path to write pathway groupings as determined by EnrichmentMap.
ENRICH_NES	(integer) NES cutoff to select validated selection-enriched pathways (default=3).
UNENRICH_NES	(integer) NES cutoff to select unenriched pathways (default=0.1).
enrich_folder	(char) path to directory to store output files (PLINK files per selection-enriched gene set).
enrichEM_folder	(char) path to directory to store output files (PLINK files per selection-enriched pathway, grouped via AutoAnnotate).
unenrich_folder	(char) path to directory to store output files (PLINK files per unenriched gene set).

Value

none

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