enrichment_analysis {MAGeCKFlute} | R Documentation |
Enrichment analysis
enrichment_analysis(geneList, universe = NULL, method = "ORT", type = "KEGG", organism = "hsa", pvalueCutoff = 0.25, qvalueCutoff = 0.2, pAdjustMethod = "BH", minGSSize = 2, maxGSSize = 50, plotTitle = NULL, color = "#3f90f7")
geneList |
A character vector or a ranked numeric vector(for GSEA) with names of geneid, specifying the genelist to do enrichment analysis. |
universe |
A character vector, specifying the backgound genelist, default is whole genome. |
method |
One of "ORT"(Over-Representing Test), "GSEA"(Gene Set Enrichment Analysis), "DAVID", "GOstats", and "HGT"(HyperGemetric test), or index from 1 to 5 |
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. |
qvalueCutoff |
Qvalue 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. |
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 <- names(geneList)[1:100] keggA = enrichment_analysis(genes, method = "HGT", type = "KEGG") print(keggA$gridPlot)