enrichDGO: Perform DO and GO enrichment analysis

In JoelleJee/DGOplot: DO and GO Enrichment Analyses Plotting

Description

A function that performs DO and GO enrichment analysis given a list of geneIDs.

Usage

enrichDGO(
  gene,
  Gont = "MF",
  Dont = "DO",
  pvalueCutoff = 0.05,
  pAdjustMethod = "BH",
  universe,
  qvalueCutoff = 0.2,
  minGSSize = 10,
  maxGSSize = 500,
  readable = FALSE,
  pool = FALSE
)

Arguments

gene	a vector of entrez gene id.
Gont	GO categories; one of "BP", "MF", "CC", or "ALL" for all three.
Dont	DO categories; one of DO or DOLite
pvalueCutoff	p-valuve cutoff
pAdjustMethod	one of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none"
universe	background genes
qvalueCutoff	q-value cutoff
minGSSize	minimal size of genes annotated by NCG category for testing
maxGSSize	maximal size of each geneSet for analyzing
readable	whether mapping gene ID to gene Name
pool	If ont='ALL', whether pool 3 GO sub-ontologies

Value

Returns a list of 2 enrichResults

• DOanalysis - an enrichResult object with DO enrichment analysis result

• GOanalysis - an enrichResult object with DO enrichment analysis result

Examples

## Not run: 
# load data from DOSE
library(DOSE)
data(geneList)
gene <- names(geneList)[abs(geneList) > 2]
result <- enrichDGO(gene, universe=names(geneList))

## End(Not run)

JoelleJee/DGOplot documentation built on July 15, 2020, 8:32 a.m.