GOtable3: GOtable3

In GoMiner: Automate the Mapping Between a List of Genes and Gene Ontology Categories

GOtable3

Description

tabulate number of geneList mappings to GO categories

Usage

GOtable3(hgncList, DB)

Arguments

hgncList	character list of gene names
DB	selected ontology branch of return value of subsetGOGOA

Value

returns a list whose components are c("DB","table","ngenes") where 'DB' is the GO DB subsetted to the desired ONTOLOGY, and 'table' is tabulation of number of occurrences of each GO category name within the desired ONTOLOGY, and ngenes is the total number of hgncList genes mapping to GOGOA

Examples

## Not run: 
# GOGOA3.RData is too large to include in the R package
# so I need to load it from a file that is not in the package.
# Since this is in a file in my own file system, I could not
# include this as a regular example in the package.
# you can generate it using the package 'minimalistGODB'
# or you can retrieve it from https://github.com/barryzee/GO/tree/main/databases
load("/Users/barryzeeberg/personal/GODB_RDATA/goa_human/GOGOA3_goa_human.RData")
x<-GOtable3(cluster52,GOGOA3$ontologies[["biological_process"]])

## End(Not run)

GoMiner documentation built on June 8, 2025, 1:29 p.m.