do_ORA_TERM2GENE: Performs over-representation analysis using Gene Ontology...

In nicohuttmann/pOmics: Framework for proteomics data analysis

Performs over-representation analysis using Gene Ontology annotations

Description

Performs over-representation analysis using Gene Ontology annotations

Usage

do_ORA_TERM2GENE(
  proteins,
  database,
  pvalueCutoff = 0.05,
  pAdjustMethod = "none",
  qvalueCutoff = 0.2,
  minGSSize = 3,
  maxGSSize = 500
)

Arguments

proteins	numeric/logical vector of proteins indicating group
database	TERM2GENE data frame
pvalueCutoff	p-value cutoff for annotations
pAdjustMethod	one of "none", "BH" (Benjamini-Hochberg correction), "hochberg", "bonferroni", "holm", "hommel", "BY", "fdr"
qvalueCutoff	q-value cutoff for annotations
minGSSize	minimum number of annotated proteins to be included
maxGSSize	maximum number of annotated proteins to be included

nicohuttmann/pOmics documentation built on Sept. 21, 2022, 9:28 a.m.