enrichModule: Module enrichment for microbiome data

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

Module enrichment for microbiome data

Description

Module enrichment for microbiome data

Usage

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

Arguments

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.

Value

A enrichResult instance.

Examples

  data(Rat_data)
  ko <- enrichModule(Rat_data)
  head(ko)

YuLab-SMU/MicrobiomeProfiler documentation built on Oct. 26, 2023, 3:55 p.m.