simpliGSEA: Perform Gene Set Enrichment Analysis

In tpq/miSciTools: Miscellaneous Science Tools for Bioinformatic Analysis

Description

This function simplifies gene set enrichment analysis for custom annotations. Do not use this function for annotations that have directed acyclic graph (DAG) relationships (e.g., GO). Gene set enrichment analysis performed using Fisher's exact test for count data. This function will automatically filter non-unique annot.genes and annot.terms pairs.

Usage

simpliGSEA(genes, universe, annot.genes, annot.terms,
  alternative = "greater")

Arguments

genes	A character vector. The gene IDs of interest.
universe	A character vector. The complete set of gene IDs used to generate the gene IDs of interest.
annot.genes	A character vector. The gene IDs to which annot.terms will correspond.
annot.terms	A character vector. The annotations corresponding to annot.genes.
alternative	A character string. Argument passed to fisher.test.

Value

A vector of unadjusted p-values named as the tested annotation.

tpq/miSciTools documentation built on Sept. 16, 2019, 4:43 p.m.