GoMiner (version 1.2)

FDR: FDR

Description

compute the false discovery rate (FDR) of the hypergeometric p values of genes mapping to gene ontology (GO) categories

Usage

FDR(sampleList, tablePop3, hyper, GOGOA3, nrand, ontology, subd, opt = 0)

Value

returns a list with FDR information

Arguments

sampleList

character vector of user-supplied genes of interest

tablePop3

return value of GOtable3()

hyper

return value of GOhypergeometric3()

GOGOA3

return value of subsetGOGOA()

nrand

integer number of randomizations

ontology

c("molecular_function","cellular_component","biological_process")

subd

character string pathname for directory containing sink.txt

opt

integer 0:1 parameter used to determine randomization method

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")
fdr<-FDR(x_sampleList1,x_tablePop31,x_hyper1,GOGOA3,3,"biological_process",tempdir(),0)
}