enrichCustomizedPathway: Enrichment of customrized pathway or annotation for any...

In Tong-Chen/YSX: For Yishengxin Training

Description

Enrichment of customrized pathway or annotation for any organism.

Usage

enrichCustomizedPathway(
  de_file,
  anno_file,
  output_prefix = NULL,
  pvalueCutoff = 0.05,
  qvalueCutoff = 0.2
)

Arguments

de_file	Two columns file with first column containing DE genes and second column with group names.
anno_file	Two columns file with first column of annotations or pathways and second columns of genes within this annotation or pathway.
output_prefix	Output prefix.
pvalueCutoff	Default 0.05
qvalueCutoff	Default 0.2
setReadable	Transfer gene ids to gene symbol. Default True.
typeL	A vector with default ad c("BP", "MF", "CC").

Examples

enrichCustomizedPathway(de_file, output_prefix=output_prefix)

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