do_ORA_MSigDB: Performs over-representation analysis using MSigDB...

In nicohuttmann/pOmics: Framework for proteomics data analysis

Performs over-representation analysis using MSigDB annotations

Description

Performs over-representation analysis using MSigDB annotations

Usage

do_ORA_MSigDB(
  proteins,
  pvalueCutoff = 0.05,
  pAdjustMethod = "none",
  qvalueCutoff = 0.2,
  minGSSize = 10,
  maxGSSize = 500,
  dataset,
  view = F,
  return.all = F,
  add.info = F
)

Arguments

proteins	numeric/logical vector of proteins indicating group
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
dataset	dataset
view	view results
return.all	return enrichResult object; useful for further analysis of enrichment results
add.info	add additional information to the results data frame

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