HTGM3Ddriver: HTGM3Ddriver

In HTGM3D: Three Dimensional High Throughput 'GoMiner'

HTGM3Ddriver

Description

driver to invoke HTGM3D()

Usage

HTGM3Ddriver(
  dir,
  geneList,
  GOGOA3,
  thresh1,
  thresh3,
  mn,
  mx,
  pcgMN,
  pcgMX,
  verbose
)

Arguments

dir	character string full path name to the directory acting as result repository
geneList	character vector of user-supplied genes of interest
GOGOA3	return value of subsetGOGOA()
thresh1	numerical acceptance threshold for individual ontologies
thresh3	numerical acceptance threshold for joint ontology
mn	integer min category size threshold passed to trimGOGOA3()
mx	integer max category size threshold passed to trimGOGOA3()
pcgMN	integer param passed to pruneCatGenes
pcgMX	integer param passed to pruneCatGenes
verbose	integer vector representing vprint classes

Details

suggested standardized class codes for vprint() -1 = developer debugging only 0 = constitutively turned on 1 = help for new user 2 = follow progress of long computation 3 = primary results 4 = meta information (e.g. dims of a matrix before and after trimming) 5 = warnings 6 = errors

Value

returns matrix containing information that provides the input needed for running plot3d()

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")

#load("data/cluster52.RData")
geneList<-cluster52
dir<-tempdir()
l3<-HTGM3Ddriver(dir,geneList,GOGOA3,thresh1=3,thresh3=3,
 mn=2,mx=20000,pcgMN=2,pcgMX=200,verbose=1:5)

## End(Not run)

HTGM3D documentation built on June 8, 2025, 11:06 a.m.