View source: R/genePathwayMatchingV2.R
pathwayMatch | R Documentation |
Takes the result of the genePatternMatch function and finds significantly enriched pathways for each pattern.
pathwayMatch(gene_list, pathways, p_threshold = 0.05, pAdjustMethod = "BH")
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") |
List of gene overlap objects, pathways with significant overlap and pathway names for each pattern
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)
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