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enrichDAVID

enrichDAVID

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

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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