enrichCOG: COG enrichment analysis for microbiome data

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

COG enrichment analysis for microbiome data

Description

COG enrichment analysis for microbiome data

Usage

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

Arguments

gene	a vector of COG ids.
dtype	one of "category", "pathway"
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 the all COGs.
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(Psoriasis_data)
cog <- enrichCOG(Psoriasis_data,dtype="category")

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