enrichKO {MicrobiomeProfiler}R Documentation

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).

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)


[Package MicrobiomeProfiler version 1.0.0 Index]