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 1.16.11 Index]