enhance_enrichGO: GO Enrichment Analysis of a gene set. Given a vector of...

In xiayh17/RNAseqStat: A Pipeline to Process RNAseq Data

GO Enrichment Analysis of a gene set. Given a vector of genes, this function will return the enrichment GO categories after FDR control.

Description

GO Enrichment Analysis of a gene set. Given a vector of genes, this function will return the enrichment GO categories after FDR control.

Usage

enhance_enrichGO(
  gene,
  OrgDb,
  keyType = "ENTREZID",
  ont = "MF",
  pvalueCutoff = 0.05,
  pAdjustMethod = "BH",
  universe,
  qvalueCutoff = 0.2,
  minGSSize = 10,
  maxGSSize = 500,
  readable = FALSE,
  pool = FALSE,
  simplify = FALSE
)

Arguments

gene	a vector of entrez gene id.
OrgDb	OrgDb
keyType	keytype of input gene
ont	One of "BP", "MF", and "CC" subontologies, or "ALL" for all three.
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.
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.
minGSSize	minimal size of genes annotated by Ontology term for testing.
maxGSSize	maximal size of genes annotated for testing
readable	whether mapping gene ID to gene Name
pool	If ont='ALL', whether pool 3 GO sub-ontologies
simplify	whether simplify

Value

An enrichResult instance.

Author(s)

Guangchuang Yu https://guangchuangyu.github.io

See Also

enrichResult-class, compareCluster

Examples

## Not run: 
  data(geneList, package = "DOSE")
	de <- names(geneList)[1:100]
	yy <- enrichGO(de, 'org.Hs.eg.db', ont="BP", pvalueCutoff=0.01)
	head(yy)

## End(Not run)

xiayh17/RNAseqStat documentation built on June 16, 2022, 11:51 a.m.