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enricher

enricher

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

statistical analysis and visualization of functional profiles for genes and gene clusters

v3.18.1
Artistic-2.0
Authors
Guangchuang Yu [aut, cre, cph] (<https://orcid.org/0000-0002-6485-8781>), Li-Gen Wang [ctb], Giovanni Dall'Olio [ctb] (formula interface of compareCluster)
Initial release

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