get_GO_annotations: Extract GO temrs information from GO annotation

In wulingyun/CopTea: Combinatorial OPTimization based Enrichment Analysis

Description

Generate the annotation matrix from an object of class "Go3AnnDbBimap" in Bioconductor annotation package.

Usage

get_GO_annotations(go.map, evidence = "ALL", category = "ALL", gene.set = NULL)

Arguments

go.map	An object of class "Go3AnnDbBimap".
evidence	Vector of string to filter the GO annotations, could be "ALL" or a set of evidence codes.
category	Vector of string to filter the GO categories, could be "ALL" or a set of GO categories.
gene.set	Vector of string to filter the genes.

Details

This function generates the annotation matrix required by enrichment analysis methods.

Value

This function returns a sparse matrix as required by enrichment analysis methods, with each row represents a gene and each column denotes a term. The row names and column names are set as the corresponding gene and term ID respectively.

See Also

netgen

Examples

## Not run: 
if (!requireNamespace("BiocManager"))
  install.packages("BiocManager")
BiocManager::install("org.Hs.eg.db")
x <- get_GO_annotations(org.Hs.egGO2ALLEGS)

## End(Not run)

wulingyun/CopTea documentation built on Dec. 4, 2019, 2:59 p.m.