enricher: enricher

In YuLab-SMU/clusterProfiler: A universal enrichment tool for interpreting omics data

enricher

Description

A universal enrichment analyzer

Usage

enricher(
  gene,
  pvalueCutoff = 0.05,
  pAdjustMethod = "BH",
  universe = NULL,
  minGSSize = 10,
  maxGSSize = 500,
  qvalueCutoff = 0.2,
  gson = NULL,
  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.
gson	a GSON object, if not NULL, use it as annotation data.
TERM2GENE	user input annotation of TERM TO GENE mapping, a data.frame of 2 column with term and gene. Only used when gson is NULL.
TERM2NAME	user input of TERM TO NAME mapping, a data.frame of 2 column with term and name. Only used when gson is NULL.

Value

A enrichResult instance

Author(s)

Guangchuang Yu https://yulab-smu.top

YuLab-SMU/clusterProfiler documentation built on Dec. 3, 2024, 1:32 p.m.