FDR: FDR

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

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)

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

Value

returns a list with FDR information

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

## End(Not run)

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