HTGM2Ddriver: HTGM2Ddriver

In HTGM2D: Two Dimensional High Throughput 'GoMiner'

HTGM2Ddriver

Description

driver to invoke GoMiner and HTGM2D, and compare the results

Usage

HTGM2Ddriver(
  dir,
  geneList,
  ontologies,
  GOGOA3,
  enrichThresh = 2,
  countThresh = 5,
  pvalThresh = 0.1,
  fdrThresh = 0.1,
  nrand = 100,
  mn,
  mx,
  opt = 0,
  verbose = 1
)

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()
enrichThresh	numerical acceptance threshold for enrichment passed to GoMiner
countThresh	numerical acceptance threshold for gene count passed to GoMiner
pvalThresh	numerical acceptance threshold for pval
fdrThresh	numerical acceptance threshold for fdr
nrand	numeric number of randomizations to compute FDR
mn	integer param passed to trimGOGOA3, min size threshold for a category
mx	integer param passed to trimGOGOA3, max size threshold for a category
opt	integer 0:1 parameter used to select randomization method
verbose	integer vector representing classes

Value

returns no value, but saves hyperlinked SVG heatmap files to a results directory

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")
geneList<-cluster52
ontologies<-c("biological_process","cellular_component")
dir<-tempdir()
HTGM2Ddriver(dir,geneList,ontologies,GOGOA3,enrichThresh=2,
 countThresh=5,pvalThresh=0.10,fdrThresh=0.10,nrand=100,mn=2,mx=2000)

## End(Not run)

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