fisherPathwayEnrichment: fisherPathwayEnrichment

In hemoshear/pathwayTalk:

fisherPathwayEnrichment

Description

Conduct Fisher's test for pathway enrichment analysis for a set of differentially expressed genes.

Usage

fisherPathwayEnrichment(DEGs, gene_alpha, pathways)

Arguments

DEGs	A dataframe of differential gene expression results with associated p-values in a column 'pvalue'. Extracted from the output of diffExpression().
gene_alpha	Significance level for differentially expressed genes. Genes with a p-value less than 'gene_alpha' will be labeled as differentially expressed for the purpose doing a Fisher's exact test for pathway enrichment.
pathways	A named list in which each element is a pathway containing a character vector of the corresponding gene IDs.

Value

A data frame of results for the Fisher's exact tests.

• p - Unadjusted p-value.

• adj_p - FDR adjusted p-value.

• estimate - Odds ratio point estimate.

• pathway - Pathway ID.

hemoshear/pathwayTalk documentation built on July 16, 2022, 12:09 a.m.