HTGM2D: HTGM2D

In HTGM2D: Two Dimensional High Throughput 'GoMiner'

HTGM2D

Description

run 2D version of GoMiner

Usage

HTGM2D(dir, geneList, ontologies, GOGOA3)

Arguments

dir	character string full path name to the directory acting as result repository
geneList	character vector of user-supplied genes of interest
ontologies	character vector of 2 ontologies e.g. c("biological_process","cellular_component")
GOGOA3	return value of subsetGOGOA()

Value

returns the return value of Jaccard()

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")
subd<-tempdir()
geneList<-cluster52
ontologies<-c("biological_process","cellular_component")
mat<-HTGM2D(subd,geneList,ontologies,GOGOA3)

## End(Not run)

HTGM2D documentation built on June 8, 2025, 9:38 p.m.