OR_msigdb: A wrapper of over-representation approach, MSigDB

In markgene/mutils: Mark's utility functions

A wrapper of over-representation approach, MSigDB

Description

Over-representation approach, MSigDB

Usage

OR_msigdb(
  gene,
  species = "Homo sapiens",
  gs_cat = "H",
  gs_subcat = NULL,
  universe = NULL,
  pvalueCutoff = 1,
  pAdjustMethod = "BH",
  minGSSize = 5,
  maxGSSize = 10000,
  qvalueCutoff = 1
)

Arguments

gene	a vector of gene symbol.
species	an one-element character vector of species. Default to "Homo sapiens".
gs_cat	an one-element character vector of gene set category. Default to Hallmark gene sets.
gs_subcat	an one-element character vector of gene set sub-category. Default to NULL.
universe	background genes. If missing, the all genes listed in the database (eg TERM2GENE table) will be used as background.
pvalueCutoff	adjusted pvalue cutoff on enrichment tests to report
pAdjustMethod	one of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none"
minGSSize	minimal size of genes annotated for testing
maxGSSize	maximal size of genes annotated for testing
qvalueCutoff	qvalue cutoff on enrichment tests to report as significant. Tests must pass i) pvalueCutoff on unadjusted pvalues, ii) pvalueCutoff on adjusted pvalues and iii) qvalueCutoff on qvalues to be reported.

Value

A enrichResult instance

Author(s)

Mark J Chen

markgene/mutils documentation built on March 23, 2022, 1:14 p.m.