KE: KEGG Pathway Enrichment analysis function

In guokai8/EnrichR: Functional Enrichment analysis

Description

KEGG Pathway Enrichment analysis function

Usage

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.