runGoMinerExamples: runGoMinerExamples

In GoMiner: Automate the Mapping Between a List of Genes and Gene Ontology Categories

runGoMinerExamples

Description

driver to run GoMiner under several randomization procedures

Usage

runGoMinerExamples(
  title = NULL,
  dir,
  sampleList,
  GOGOA3,
  ontology,
  enrichThresh = 2,
  countThresh = 5,
  pvalThresh = 0.1,
  fdrThresh = 0.1,
  nrand = 2,
  mn = 2,
  mx = 200,
  verbose = 1
)

Arguments

title	character string descriptive title
dir	character string full pathname to the directory acting result repository
sampleList	character list of gene names
GOGOA3	return value of subsetGOGOA()
ontology	character string c("molecular_function", "cellular_component", "biological_process")
enrichThresh	numerical acceptance threshold for enrichment
countThresh	numerical acceptance threshold for gene count
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
verbose	integer vector representing classes

Value

returns a list containing the return value of GoMiner()

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")
ontology<-"biological_process"
t<-sort(table(GOGOA3$ontologies[[ontology]][,"HGNC"]),decreasing=TRUE)
dir<-tempdir()

sampleList<-names(t)[1:50]
title<-"hi_hitters"
hh<-runGoMinerExamples(title,dir,sampleList,GOGOA3,ontology,nrand=5)

sampleList<-names(t)[1001:1050]
title<-"hi_hitters5"
hh<-runGoMinerExamples(title,dir,sampleList,GOGOA3,ontology,nrand=5)

sampleList<-cluster52
title<-"cluster52"
hh<-runGoMinerExamples(title,dir,sampleList,GOGOA3,ontology,nrand=5)

## End(Not run)

GoMiner documentation built on June 8, 2025, 1:29 p.m.