enrichCOG {MicrobiomeProfiler} | R Documentation |
COG enrichment analysis for microbiome data
enrichCOG( gene, pvalueCutoff = 0.05, pAdjustMethod = "BH", universe, minGSSize = 10, maxGSSize = 500, qvalueCutoff = 0.2 )
gene |
a vector of COG ids. |
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 the all COGs. |
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(Psoriasis_data) cog <- enrichCOG(Psoriasis_data)