enrichKO: KO enrichment for microbiome data

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

KO enrichment for microbiome data

Description

KO enrichment for microbiome data

Usage

enrichKO(
  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) or EC id (e.g. 1.1.1.27).
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 <- enrichKO(Rat_data)
  head(ko)

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