enricher_internal: enrich.internal
In YuLab-SMU/DOSE: Disease Ontology Semantic and Enrichment analysis

enricher_internal

R Documentation

enrich.internal

Description

interal method for enrichment analysis

Usage

enricher_internal(
  gene,
  pvalueCutoff,
  pAdjustMethod = "BH",
  universe = NULL,
  minGSSize = 10,
  maxGSSize = 500,
  qvalueCutoff = 0.2,
  USER_DATA
)

Arguments

`gene`	a vector of entrez gene id.
`pvalueCutoff`	Cutoff value of pvalue.
`pAdjustMethod`	one of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none"
`universe`	background genes, default is the intersection of the 'universe' with genes that have annotations. Users can set ‘options(enrichment_force_universe = TRUE)' to force the ’universe' untouched.
`minGSSize`	minimal size of genes annotated by Ontology term for testing.
`maxGSSize`	maximal size of each geneSet for analyzing
`qvalueCutoff`	cutoff of qvalue
`USER_DATA`	ontology information