checkGeneListVsDB: checkGeneListVsDB

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

checkGeneListVsDB

Description

determine if gene list and database contain compatible identifiers

Usage

checkGeneListVsDB(geneList, ontology, GOGOA3, thresh = 0.5, verbose = FALSE)

Arguments

geneList	character list of gene names
ontology	character string c("molecular_function", "cellular_component", "biological_process")
GOGOA3	return value of subsetGOGOA()
thresh	numeric acceptance threshold for fraction of gene list matching database identifiers
verbose	integer vector representing classes

Value

returns no value, but may have side effect of aborting the computation

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")
checkGeneListVsDB(geneList=cluster52,ontology="biological_process",
 GOGOA3,thresh=0.5,verbose=TRUE)

# supposed to generate error message
load("/Users/barryzeeberg/personal/GODB_RDATA/sgd/GOGOA3_sgd.RData")
checkGeneListVsDB(geneList=xenopusGenes,ontology="biological_process",
 GOGOA3,thresh=0.5,verbose=TRUE)

## End(Not run)

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