RE: Reactome Pathway Enrichment analysis function

In guokai8/EnrichR: Functional Enrichment analysis

Description

Reactome Pathway Enrichment analysis function

Usage

RE(
  df,
  RO_FILE,
  keytype = "SYMBOL",
  species = "human",
  padj.method = "BH",
  minSize = 2,
  maxSize = 500,
  keepRich = TRUE,
  filename = NULL,
  cutoff = 0.05
)

Arguments

df	DGE files (DESeq2 result files) or vector contains gene names
RO_FILE	Reactome annotation data
species	species name
padj.method	p value adjust method (default: BH)
minSize	minimal number of genes included in significant terms
maxSize	maximum number of genes included in significant terms
keepRich	keep terms with rich factor value equal 1 or not (default: TRUE)
filename	output filename
cutoff	cutoff value for filtering significant terms (default: 0.05)
gene.cutoff	the cut-off value for select DEGs (default: 0.01)

Author(s)

Kai Guo

guokai8/EnrichR documentation built on May 18, 2020, 5:29 a.m.