HTGM: HTGM

In HTGM: High Throughput 'GoMiner'

HTGM

Description

driver to invoke GoMiner for multiple studies, and integrate the results in a categories versus study hyperlinked heatmap

Usage

HTGM(
  title = NULL,
  dir = tempdir(),
  sampleLists,
  GOGOA3,
  ONT,
  enrichThresh = 2,
  countThresh = 5,
  fdrThresh = 0.1,
  nrand = 100,
  mn = 2,
  mx = 200,
  opt = 0,
  verbose = 1
)

Arguments

title	character string descriptive title
dir	character string full pathname to the directory acting as result repository
sampleLists	list of character vector of user-supplied genes of interest
GOGOA3	return value of subsetGOGOA()
ONT	c("molecular_function","cellular_component","biological_process")
enrichThresh	numerical acceptance threshold for enrichment passed to GoMiner
countThresh	numerical acceptance threshold for gene count passed to GoMiner
fdrThresh	numerical acceptance threshold for fdr passed to GoMiner
nrand	integer number of randomizations passed to GoMiner
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 parameter passed to vprint()

Value

returns the matrix of significant categories versus study

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/Housekeeping_Genes.RData")
sampleList<-unique(as.matrix(Housekeeping_Genes[,"Gene.name"]))
n<-nrow(sampleList)
sampleLists<-list()
# test the effect of random sampling of the entire gene set
# this can give an idea of the quality of the GoMiner results
# when the complete gene set is yet to be determined
sampleLists[["1"]]<-sampleList[sample(n,n/2)]
sampleLists[["2"]]<-sampleList[sample(n,n/2)]
sampleLists[["3"]]<-sampleList[sample(n,n/2)]
sampleLists[["4"]]<-sampleList[sample(n,n/2)]
sampleLists[["5"]]<-sampleList[sample(n,n/2)]
sampleLists[["ALL"]]<-sampleList
m<-HTGM(title=NULL,dir=tempdir(),sampleLists,GOGOA3,ONT="biological_process",
 enrichThresh=2,countThresh=5,fdrThresh=0.10,nrand=100)

## End(Not run)

HTGM documentation built on June 8, 2025, 10:10 a.m.