enrich.DAVID {MAGeCKFlute}R Documentation

Do enrichment analysis using DAVID

Description

an update version of DAVIDWebService to do enrichment analysis

Usage

enrich.DAVID(gene, universe = NULL, david.user, idType = "ENTREZ_GENE_ID",
  minGSSize = 2, maxGSSize = 500, annotation = "GOTERM_BP_FAT",
  pvalueCutoff = 0.25, pAdjustMethod = "BH", qvalueCutoff = 0.2)

Arguments

gene

Character vector, specifying the genelist to do enrichment analysis.

universe

Character vector, specifying the backgound genelist, default is whole genome.

david.user

Character, specifying a valid DAVID user account.

idType

Character, indicating the gene id type of input genelist, such as "ENTREZ_GENE_ID"(default).

minGSSize

Minimal size of each geneSet for testing.

maxGSSize

Maximal size of each geneSet for analyzing.

annotation

Geneset category for testing, GOTERM_BP_FAT(default).

pvalueCutoff

Pvalue cutoff.

pAdjustMethod

One of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none".

qvalueCutoff

Qvalue cutoff.

Value

A enrichResult instance.

Author(s)

Wubing Zhang

See Also

enrich.HGT

enrich.GOstats

enrich.GSE

enrich.ORT

enrichment_analysis

enrichResult-class

Examples

data(geneList, package = "DOSE")
genes <- names(geneList)[1:100]
## Not run: 
	# Before running this example, you need to have a david account.
	enrichRes <- enrich.DAVID(genes, david.user="david.user@edu.com")
	head(enrichRes@result)

## End(Not run)

[Package MAGeCKFlute version 1.0.1 Index]