enricher: enricher

Description Usage Arguments Value Author(s)

View source: R/enricher.R

Description

A universal enrichment analyzer

Usage

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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.