enrichHMDB {MicrobiomeProfiler} | R Documentation |
Metabolism enrichment analysis for microbiome data
enrichHMDB( metabo_list, pvalueCutoff = 0.05, pAdjustMethod = "BH", universe, minGSSize = 10, maxGSSize = 500, qvalueCutoff = 0.2 )
metabo_list |
a vector of metabolites in HMDB.ID |
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 HMDB db. |
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.
x1 <- bitr_smpdb(c("PW_C000164","PW_C000078","PW_C000040"), from_Type = "Metabolite.ID",to_Type = "HMDB.ID") x2 <- enrichHMDB(x1$HMDB.ID)