enrichKO {MicrobiomeProfiler} | R Documentation |
KO enrichment for microbiome data
enrichKO( gene, pvalueCutoff = 0.05, pAdjustMethod = "BH", universe, minGSSize = 10, maxGSSize = 500, qvalueCutoff = 0.2 )
gene |
a vector of K gene id (e.g. K00001). |
pvalueCutoff |
adjusted pvalue cutoff on enrichment tests to report. |
pAdjustMethod |
one of "holm","hochberg","hommel","bonferroni","BH", "BY","fdr","none". |
universe |
universe background genes. If missing, use all K genes. |
minGSSize |
minimal size of genes annotated by KEGG term for testing. |
maxGSSize |
maximal size of genes annotated for testing. |
qvalueCutoff |
qvalue cutoff on enrichment tests to report. |
A enrichResult
instance.
data(Rat_data) ko <- enrichKO(Rat_data) head(ko)