enrichedGO: Enriched Gene Ontology terms used as example

In jianhong/ChIPpeakAnno: Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments, or any experiments that result in large number of genomic interval data

Enriched Gene Ontology terms used as example

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)

jianhong/ChIPpeakAnno documentation built on Nov. 1, 2024, 8:55 a.m.