enrich.GOstats {MAGeCKFlute} | R Documentation |
Do enrichment analysis using GOstats method
enrich.GOstats(gene, universe = NULL, type = c("KEGG", "BP", "MF", "CC"), organism = "hsa", pvalueCutoff = 0.25, pAdjustMethod = "BH")
gene |
A character vector, specifying the genelist to do enrichment analysis. |
universe |
A character vector, specifying the backgound genelist, default is whole genome. |
type |
Geneset category for testing, KEGG(default). |
organism |
A character, specifying organism, such as "hsa" or "Human"(default), and "mmu" or "Mouse" |
pvalueCutoff |
Pvalue cutoff. |
pAdjustMethod |
One of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none". |
A enrichResult instance.
Wubing Zhang
data(geneList, package = "DOSE") genes <- names(geneList)[1:100] ## Not run: enrichRes <- enrich.GOstats(genes, type="BP") head(enrichRes@result) ## End(Not run)