diffAnaComputeFDR: Computes the FDR corresponding to the p-values of the...

In samWieczorek/DAPAR: Tools for the Differential Analysis of Proteins Abundance with R

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

utils::data(Exp1_R25_prot, package='DAPARdata')
obj <- Exp1_R25_prot[1:1000]
level <- obj@experimentData@other$typeOfData
metacell.mask <- match.metacell(GetMetacell(obj), 'missing', level)
indices <- GetIndices_WholeMatrix(metacell.mask, op='>=', th=1)
obj <- MetaCellFiltering(obj, indices, cmd='delete')
qData <- Biobase::exprs(obj$new)
sTab <- Biobase::pData(obj$new)
limma <- limmaCompleteTest(qData,sTab)
diffAnaComputeFDR(limma$logFC[,1],limma$P_Value[,1])

samWieczorek/DAPAR documentation built on May 6, 2022, 5:30 p.m.