HTGM2D (version 1.1.1)

HTGM2Ddriver: 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
)

Value

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

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

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.
# 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)
}