GoMiner (version 1.2)

RCPD: RCPD

Description

prepare a cpd of p values from randomized gene sets

Usage

RCPD(GOGOA3, tablePop, geneList, nrand, ontology, hyper, subd, opt)

Value

returns a histogram of log10(p)

Arguments

GOGOA3

return value of subsetGOGOA()

tablePop

return value of GOtable3()

geneList

character vector lisgt of genes to randomize

nrand

integer number of randomizations

ontology

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

hyper

return value of GOhypergeometric3() from real (nonrandom) data

subd

character string pathname for directory containing sink.txt

opt

integer 0:1 parameter used to select randomization method

Details

the cpd of the randomizations is to be used for estimating the false discovery rate (FDR) of the real sampled genes

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")
rcpd<-RCPD(GOGOA3,x_tablePop31,10,3,"biological_process",x_hyper1,tempdir(),0)
}