DAPAR (version 1.4.7)

diffAnaComputeFDR: 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(data, threshold_PVal = 0, threshold_LogFC = 0, pi0Method = 1)

Arguments

data

The result of the differential analysis processed by diffAna

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)

Examples

data(UPSpep25)
obj <- wrapper.mvImputation(UPSpep25, "QRILC")
condition1 <- '25fmol'
condition2 <- '10fmol'
qData <- Biobase::exprs(obj)
samplesData <- Biobase::pData(obj)
labels <- Biobase::pData(obj)[,"Label"]
limma <- diffAnaLimma(qData,samplesData, labels, condition1, condition2)
diffAnaComputeFDR(limma)