enrichMDA: Microbe-Disease associations enrichment analysis

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

Microbe-Disease associations enrichment analysis

Description

Microbe-Disease associations enrichment analysis

Usage

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

Arguments

microbe_list	a vector of microbe ncbi tax ids.
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 disbiome as default.
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(microbiota_taxlist)
mda <- enrichMDA(microbiota_taxlist)
head(mda)

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