RCPD: RCPD

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

RCPD

Description

prepare a cpd of p values from randomized gene sets

Usage

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

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

Value

returns a histogram of log10(p)

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

## End(Not run)

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