GoMiner: GoMiner

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

GoMiner

Description

driver to generate heatmap

Usage

GoMiner(
  title = NULL,
  dir,
  sampleList,
  GOGOA3,
  ONT,
  enrichThresh = 2,
  countThresh = 5,
  fdrThresh = 0.1,
  nrand = 100
)

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()
ONT	character string c("molecular_function", "cellular_component", "biological_process")
enrichThresh	numerical acceptance threshold for enrichment
countThresh	numerical acceptance threshold for gene count
fdrThresh	numerical acceptance threshold for fdr
nrand	numeric number of randomizations to compute FDR

Value

returns a matrix suitable to generate a heatmap

Examples

## Not run: 
# GOGOA3.RData is too large to include in the R package
# you can generate it using the package 'minimalistGODB'
# or you can retrieve it from https://github.com/barryzee/GO
load("~/GODB_RDATA/GOGOA3.RData")
load("data/cluster52.RData")
l<-GoMiner("Cluster52",tempdir(),cluster52,
 GOGOA3,ONT="biological_process",enrichThresh=2,
 countThresh=5,fdrThresh=0.10,nrand=10)

## End(Not run)

GoMiner documentation built on April 12, 2025, 1:43 a.m.