diffAnaComputeFDR: Computes the FDR corresponding to the p-values of the...
In DAPAR: Tools for the Differential Analysis of Proteins Abundance with R

Description Usage Arguments Value Author(s) Examples

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}..

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

`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`

The computed FDR value (floating number)

Samuel Wieczorek

utils::data(Exp1_R25_pept, package='DAPARdata')
obj <- Exp1_R25_pept[1:1000]
keepThat <- mvFilterGetIndices(obj, condition='WholeMatrix', threshold=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])