enrichKEGG_model: KEGG enrichment for model organism.

In Tong-Chen/YSX: For Yishengxin Training

Description

KEGG enrichment for model organism.

Usage

enrichKEGG_model(
  de_file,
  org_db = "org.Hs.eg.db",
  output_prefix = NULL,
  organism = "human",
  pvalueCutoff = 0.05,
  qvalueCutoff = 0.2,
  setReadable = TRUE
)

Arguments

org_db	R annotation package like org.Hs.eg.db.
output_prefix	Output prefix.
organism	KEGG supported organisms like human, mouse.
pvalueCutoff	Default 0.05
qvalueCutoff	Default 0.2
setReadable	Transfer gene ids to gene symbol. Default True.
Two	columns file with first column containing DE genes and second column with group names.

Value

A dataframe containing top 10 enriched terms.

Examples

enrichKEGG_model(de_file, output_prefix=output_prefix)

Tong-Chen/YSX documentation built on Jan. 25, 2021, 2:49 a.m.