diffAnaComputeAdjustedPValues: Computes the adjusted p-values

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

Computes the adjusted p-values

Description

This function is a wrapper 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

diffAnaComputeAdjustedPValues(pval, pi0Method = 1)

Arguments

pval	The result (p-values) of the differential analysis processed by limmaCompleteTest
pi0Method	The parameter pi0.method of the method adjust.p in the package cp4p

Value

The computed adjusted p-values

Author(s)

Samuel Wieczorek

Examples

data(Exp1_R25_prot, package="DAPARdata")
obj <- Exp1_R25_prot[seq_len(1000)]
level <- 'protein'
metacell.mask <- match.metacell(GetMetacell(obj), c("Missing POV", "Missing MEC"), 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)
df <- data.frame(id = rownames(limma$logFC), logFC = limma$logFC[, 1], pval = limma$P_Value[, 1])

diffAnaComputeAdjustedPValues(pval = limma$P_Value[, 1])

prostarproteomics/DAPAR documentation built on Oct. 11, 2024, 12:03 p.m.