GoMiner (version 1.2)

hitterBeforeAfterDriver: hitterBeforeAfterDriver

Description

driver to invoke hitters2() and trimGOGOA3()

Usage

hitterBeforeAfterDriver(GOGOA3, mn = 20, mx = 200, verbose)

Value

returns the return value of trimGOGOA3()

Arguments

GOGOA3

return value of minimalistGODB::buildGODatabase()

mn

integer minimum category size

mx

integer maximum category size

verbose

integer vector representing classes

Examples

if (FALSE) {
# 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.
# This example is given in full detail in the package vignette.
# You can generate GOGOA3.RData using the package 'minimalistGODB'
# or you can retrieve it from https://github.com/barryzee/GO
dir<-"/Users/barryzeeberg/personal/GODB_RDATA/goa_human/"
load(sprintf("%s/%s",dir,"GOGOA3_goa_human.RData"))
geneList<-GOGOA3$ontologies[["biological_process"]][1:10,"HGNC"]
GOGOA3tr<-hitterBeforeAfterDriver(GOGOA3,mn=20,mx=200,1)
}