enricher: enricher

In clusterProfiler: statistical analysis and visualization of functional profiles for genes and gene clusters

Description

A universal enrichment analyzer

Usage

enricher(
  gene,
  pvalueCutoff = 0.05,
  pAdjustMethod = "BH",
  universe,
  minGSSize = 10,
  maxGSSize = 500,
  qvalueCutoff = 0.2,
  TERM2GENE,
  TERM2NAME = NA
)

Arguments

gene	a vector of gene id
pvalueCutoff	adjusted pvalue cutoff on enrichment tests to report
pAdjustMethod	one of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none"
universe	background genes. If missing, the all genes listed in the database (eg TERM2GENE table) will be used as background.
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.
TERM2GENE	user input annotation of TERM TO GENE mapping, a data.frame of 2 column with term and gene
TERM2NAME	user input of TERM TO NAME mapping, a data.frame of 2 column with term and name

Value

A enrichResult instance

Author(s)

Guangchuang Yu

clusterProfiler documentation built on Feb. 11, 2021, 2:02 a.m.