EnrichAnalyzer {MAGeCKFlute} | R Documentation |
Enrichment analysis
EnrichAnalyzer( geneList, keytype = "Symbol", type = "Pathway+GOBP", method = "HGT", organism = "hsa", pvalueCutoff = 0.25, limit = c(2, 200), universe = NULL, filter = FALSE, gmtpath = NULL, verbose = TRUE )
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'). |
method |
One of "ORT"(Over-Representing Test), "GSEA"(Gene Set Enrichment Analysis), and "HGT"(HyperGemetric test). |
organism |
'hsa' or 'mmu'. |
pvalueCutoff |
FDR cutoff. |
limit |
A two-length vector (default: c(2, 200)), 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. |
verbose |
Boolean |
enrichRes
is an enrichResult instance.
Wubing Zhang
data(geneList, package = "DOSE") ## Not run: keggA = EnrichAnalyzer(geneList[1:500], keytype = "entrez") head(keggA@result) ## End(Not run)