pathwayMatch: Matches list of genes to pathways

In FertigLab/ATACCoGAPS: Analysis Tools for scATACseq Data with CoGAPS

Matches list of genes to pathways

Description

Takes the result of the genePatternMatch function and finds significantly enriched pathways for each pattern.

Usage

pathwayMatch(gene_list, pathways, p_threshold = 0.05, pAdjustMethod = "BH")

Arguments

gene_list	Result from the genePatternMatch function, a list of genes for each pattern
pathways	List of pathways to perform gene enrichment on. Recommended to download using msigdbr (see examples)
p_threshold	significance level to use in enrichment analysis
pAdjustMethod	multiple testing correction method to apply using the p.adjust options (e.g. "BH")

Value

List of gene overlap objects, pathways with significant overlap and pathway names for each pattern

Examples

data(schepCogapsResult)
data(schepGranges)
library(Homo.sapiens)

genes <- genePatternMatch(cogapsResult = schepCogapsResult,
 generanges = schepGranges, genome = Homo.sapiens)

library(dplyr)
pathways = msigdbr::msigdbr(species = "Homo sapiens", category ="H") %>% 
dplyr::select(gs_name, gene_symbol) %>% as.data.frame()

matchedPathways = pathwayMatch(genes, pathways, p_threshold = 0.001)

FertigLab/ATACCoGAPS documentation built on Feb. 8, 2023, 6:46 p.m.