enrichment_analysis {MAGeCKFlute} | R Documentation |
Enrichment analysis
enrichment_analysis(geneList, method = "HGT", keytype = "Entrez", type = "KEGG", organism = "hsa", pvalueCutoff = 0.25, pAdjustMethod = "BH", limit = c(3, 50), universe = NULL, plotTitle = NULL, color = "#3f90f7")
geneList |
A numeric vector with gene as names. |
method |
One of "ORT"(Over-Representing Test), "GSEA"(Gene Set Enrichment Analysis), and "HGT"(HyperGemetric test). |
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). |
organism |
'hsa' or 'mmu'. |
pvalueCutoff |
Pvalue cutoff. |
pAdjustMethod |
One of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none". |
limit |
A two-length vector (default: c(3, 50)), specifying the minimal and maximal size of gene sets for enrichent analysis. |
universe |
A character vector, specifying the backgound genelist, default is whole genome. |
plotTitle |
Same as 'title' in 'plot'. |
color |
Color of points. |
A list, including two items, gridPlot
and enrichRes
. gridPlot
is
a ggplot object, and enrichRes
is a enrichResult instance.
Feizhen Wu
data(geneList, package = "DOSE") genes <- geneList[1:100] keggA = enrichment_analysis(genes, method = "HGT", type = "KEGG") print(keggA$gridPlot)