diffAnaComputeFDR {DAPAR} | R Documentation |
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 |
pval |
The result (p-values) of the differential analysis processed
by |
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 |
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])