enrich.DAVID {MAGeCKFlute} | R Documentation |
an update version of DAVIDWebService to do enrichment analysis
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)
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. |
A enrichResult instance.
Wubing Zhang
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)