enrichMDA {MicrobiomeProfiler} | R Documentation |
Microbe-Disease associations enrichment analysis
enrichMDA( microbe_list, pvalueCutoff = 0.05, pAdjustMethod = "BH", universe, minGSSize = 10, maxGSSize = 500, qvalueCutoff = 0.2 )
microbe_list |
a vector of microbe ncbi tax 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 disbiome as default. |
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(microbiota_taxlist) mda <- enrichMDA(microbiota_taxlist) head(mda)