RE: Reactome Pathway Enrichment analysis function

Description Usage Arguments Author(s)

View source: R/RE.R

Description

Reactome Pathway Enrichment analysis function

Usage

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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 16, 2020, 10:24 p.m.