GoMiner (version 1.2)

checkGeneListVsDB: checkGeneListVsDB

Description

determine if gene list and database contain compatible identifiers

Usage

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

Value

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

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

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")
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)
}