enrichGO2: GO Enrichment Analysis of a gene set.

In xiayh17/RNAseqStat2: A Pipeline to Process RNAseq Data

GO Enrichment Analysis of a gene set.

Description

Given a vector of genes, this function will return the enrichment GO categories after FDR control. enrichGO only support OrgDb and enricher is too simple for GO. In this case, a modified version of enrichGO here

Usage

enrichGO2(
  gene,
  TERM2GENE,
  TERM2NAME = NA,
  organism = "UNKNOW",
  keyType = "SYMBOL",
  ont = "ALL",
  pvalueCutoff = 0.05,
  pAdjustMethod = "BH",
  universe,
  qvalueCutoff = 0.2,
  minGSSize = 10,
  maxGSSize = 500,
  pool = FALSE
)

Arguments

gene	a vector of entrez gene id.
TERM2GENE	user input annotation of TERM TO GENE mapping, a data.frame of 2 column with term and gene
TERM2NAME	user input of TERM TO NAME mapping, a data.frame of 2 column with term and name
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
pool	If ont='ALL', whether pool 3 GO sub-ontologies

Value

An enrichResult instance.

Examples

## Not run: 
 enrichGO2(gene,TERM2GENE,TERM2NAME)

## End(Not run)

xiayh17/RNAseqStat2 documentation built on May 27, 2023, 12:13 p.m.