enrichDAVID: enrichDAVID

Description Usage Arguments Value Author(s)

View source: R/enrichDAVID.R

Description

enrichment analysis by DAVID

Usage

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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.