enrichDAVID: enrichDAVID

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

Description

enrichment analysis by DAVID

Usage

enrichDAVID(
  gene,
  idType = "ENTREZ_GENE_ID",
  universe,
  minGSSize = 10,
  maxGSSize = 500,
  annotation = "GOTERM_BP_FAT",
  pvalueCutoff = 0.05,
  pAdjustMethod = "BH",
  qvalueCutoff = 0.2,
  species = NA,
  david.user
)

Arguments

gene	input gene
idType	id type
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
annotation	david annotation
pvalueCutoff	adjusted pvalue cutoff on enrichment tests to report
pAdjustMethod	one of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none"
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.
species	species
david.user	david user

Value

A enrichResult instance

Author(s)

Guangchuang Yu

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