diffAnaComputeFDR {DAPAR}R Documentation

Computes the FDR corresponding to the p-values of the differential analysis using

Description

This function is a wrappper to the function adjust.p from the cp4p package. It returns the FDR corresponding to the p-values of the differential analysis. The FDR is computed with the function p.adjust{stats}..

Usage

diffAnaComputeFDR(logFC, pval, threshold_PVal = 0, threshold_LogFC = 0,
  pi0Method = 1)

Arguments

logFC

The result (logFC values) of the differential analysis processed by limmaCompleteTest

pval

The result (p-values) of the differential analysis processed by limmaCompleteTest

threshold_PVal

The threshold on p-pvalue to distinguish between differential and non-differential data

threshold_LogFC

The threshold on log(Fold Change) to distinguish between differential and non-differential data

pi0Method

The parameter pi0.method of the method adjust.p in the package cp4p

Value

The computed FDR value (floating number)

Author(s)

Samuel Wieczorek

Examples

require(DAPARdata)
data(Exp1_R25_pept)
obj <- Exp1_R25_pept[1:1000]
keepThat <- mvFilterGetIndices(obj, 'wholeMatrix', ncol(obj))
obj <- mvFilterFromIndices(obj, keepThat)
qData <- Biobase::exprs(obj)
sTab <- Biobase::pData(obj)
limma <- limmaCompleteTest(qData,sTab)
diffAnaComputeFDR(limma$logFC[,1],limma$P_Value[,1])

[Package DAPAR version 1.16.0 Index]