Description Usage Arguments Value Author(s) See Also Examples
Do enrichment analysis using over-representation test
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geneList |
A numeric vector with gene as names. |
keytype |
"Entrez" or "Symbol". |
type |
Molecular signatures for testing, available datasets include Pathway (KEGG, REACTOME, C2_CP), GO (GOBP, GOCC, GOMF), MSIGDB (C1, C2 (C2_CP (C2_CP_PID, C2_CP_BIOCARTA), C2_CGP), C3 (C3_MIR, C3_TFT), C4, C6, C7, HALLMARK) and Complex (CORUM). Any combination of them are also accessible (e.g. 'GOBP+GOMF+KEGG+REACTOME'). |
organism |
'hsa' or 'mmu'. |
pvalueCutoff |
FDR cutoff. |
limit |
A two-length vector, specifying the minimal and maximal size of gene sets for enrichent analysis. |
universe |
A character vector, specifying the backgound genelist, default is whole genome. |
gmtpath |
The path to customized gmt file. |
verbose |
Boolean |
... |
Other parameter |
An enrichedResult instance.
Wubing Zhang
1 2 3 4 | data(geneList, package = "DOSE")
genes <- geneList[1:100]
enrichedRes <- enrich.ORT(genes, keytype = "entrez")
head(slot(enrichedRes, "result"))
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