GE: GO Enrichment analysis function

Description Usage Arguments Author(s)

View source: R/GE.R

Description

GO Enrichment analysis function

Usage

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
GE(
  df,
  GO_FILE,
  OP = "BP",
  gene.cutoff = 0.01,
  minSize = 2,
  maxSize = 500,
  keepRich = TRUE,
  filename = NULL,
  padj.method = "BH",
  cutoff = 0.05
)

Arguments

df

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

GO_FILE

GO annotation data

OP

use BP,CC or MF

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)

filename

output filename

padj.method

p value adjust method (default: BH)

cutoff

cutoff value for filtering significant terms (default: 0.05)

Author(s)

Kai Guo


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