enrichSMPDB: Metabolism enrichment analysis for microbiome data

In YuLab-SMU/MicrobiomeProfiler: An R/shiny package for microbiome functional enrichment analysis

Metabolism enrichment analysis for microbiome data

Description

Metabolism enrichment analysis for microbiome data

Usage

enrichSMPDB(
  metabo_list,
  pvalueCutoff = 0.05,
  pAdjustMethod = "BH",
  universe,
  minGSSize = 10,
  maxGSSize = 500,
  qvalueCutoff = 0.2
)

Arguments

metabo_list	a vector of metabolites in smpdb Metabolite.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 SMPDB 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.

Value

A enrichResult instance.

Examples

smp <- enrichSMPDB(c("PW_C000164","PW_C000078","PW_C000040"))
head(smp)

YuLab-SMU/MicrobiomeProfiler documentation built on Oct. 30, 2024, 2:20 p.m.