enrichedGO: Enriched Gene Ontology terms used as example

In LihuaJulieZhu/ChIPpeakAnno: Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome ranges

Description

Enriched Gene Ontology terms used as example

Usage

enrichedGO

Format

A list of 3 dataframes.

list("bp")

dataframe described the enriched biological process with 9 columns

go.id:GO biological process id

go.term:GO biological process term

go.Definition:GO biological process description

Ontology: Ontology branch, i.e. BP for biological process

count.InDataset: count of this GO term in this dataset

count.InGenome: count of this GO term in the genome

pvalue: pvalue from the hypergeometric test

totaltermInDataset: count of all GO terms in this dataset

totaltermInGenome: count of all GO terms in the genome

list("mf")

dataframe described the enriched molecular function with the following 9 columns

go.id:GO molecular function id

go.term:GO molecular function term

go.Definition:GO molecular function description

Ontology: Ontology branch, i.e. MF for molecular function

count.InDataset: count of this GO term in this dataset

count.InGenome: count of this GO term in the genome

pvalue: pvalue from the hypergeometric test

totaltermInDataset: count of all GO terms in this dataset

totaltermInGenome: count of all GO terms in the genome

list("cc")

dataframe described the enriched cellular component the following 9 columns

go.id:GO cellular component id

go.term:GO cellular component term

go.Definition:GO cellular component description

Ontology: Ontology type, i.e. CC for cellular component

count.InDataset: count of this GO term in this dataset

count.InGenome: count of this GO term in the genome

pvalue: pvalue from the hypergeometric test

totaltermInDataset: count of all GO terms in this dataset

totaltermInGenome: count of all GO terms in the genome

Author(s)

Lihua Julie Zhu

Examples

data(enrichedGO)
dim(enrichedGO$mf)
dim(enrichedGO$cc)
dim(enrichedGO$bp)

LihuaJulieZhu/ChIPpeakAnno documentation built on Aug. 5, 2020, 12:02 a.m.