KE: KEGG Pathway Enrichment analysis function

Description Usage Arguments

View source: R/KE.R

Description

KEGG Pathway Enrichment analysis function

Usage

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KE(
  df,
  KO_FILE,
  filename = NULL,
  gene.cutoff = 0.01,
  minSize = 2,
  maxSize = 500,
  keepRich = TRUE,
  padj.method = "BH",
  cutoff = 0.05,
  builtin = TRUE
)

Arguments

df

DGE files (DESeq2 result files) or vector contains gene names

KO_FILE

KEGG annotation data

filename

output filename

gene.cutoff

the cut-off value for select DEGs (default: 0.01)

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)

padj.method

p value adjust method (default: BH)

cutoff

cutoff value for filtering significant terms (default: 0.05)

bulitin

use KEGG bulit in KEGG annotation or not(set FALSE if you want use newest KEGG data)


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