EnrichAnalyzer {MAGeCKFlute} | R Documentation |
Enrichment analysis
EnrichAnalyzer(geneList, keytype = "Entrez", type = "CORUM+KEGG", method = "ORT", organism = "hsa", pvalueCutoff = 0.25, limit = c(1, 120), universe = NULL, filter = TRUE, gmtpath = NA)
geneList |
A numeric vector with gene as names. |
keytype |
"Entrez" or "Symbol". |
type |
Geneset category for testing, one of 'CORUM', 'CPX' (ComplexPortal), 'GOBP', 'GOMF', 'GOCC', 'KEGG', 'BIOCARTA', 'REACTOME', 'WikiPathways', 'EHMN', 'PID', or any combination of them (e.g. 'GOBP+GOMF+CORUM'), or 'All' (all categories). |
method |
One of "ORT"(Over-Representing Test), "GSEA"(Gene Set Enrichment Analysis), and "HGT"(HyperGemetric test). |
organism |
'hsa' or 'mmu'. |
pvalueCutoff |
Pvalue cutoff. |
limit |
A two-length vector (default: c(1, 120)), specifying the minimal and maximal size of gene sets for enrichent analysis. |
universe |
A character vector, specifying the backgound genelist, default is whole genome. |
filter |
Boolean, specifying whether filter out redundancies from the enrichment results. |
gmtpath |
The path to customized gmt file. |
enrichRes
is an enrichResult instance.
Wubing Zhang
data(geneList, package = "DOSE") keggA = EnrichAnalyzer(geneList[1:500], method = "HGT") head(keggA@result)