enrich.HGT {MAGeCKFlute} | R Documentation |
Do enrichment analysis using Hypergeometric test
enrich.HGT(gene, universe = NULL, type = "KEGG", organism = "hsa", pvalueCutoff = 0.25, pAdjustMethod = "BH", minGSSize = 2, maxGSSize = 500)
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". |
minGSSize |
Minimal size of each geneSet for testing. |
maxGSSize |
Maximal size of each geneSet for analyzing. |
A enrichResult instance.
Feizhen Wu
data(geneList, package = "DOSE") genes <- names(geneList)[1:100] enrichRes <- enrich.HGT(genes) head(enrichRes@result)