adjustProteinLevel {MSstatsPTM}R Documentation

Adjust differential analysis result with respect to protein abundance

Description

adjustProteinLevel performs the adjustment with respect to protein abundance.

Usage

adjustProteinLevel(diffSite, diffProtein)

Arguments

diffSite

A data frame for the differential analysis result of PTMs, returned by the function extractMeanDiff with the option perProtein=FALSE. The data frame contains columns of Protein, Site, Label, log2FC, SE, Tvalue, DF, and pvalue.

diffProtein

A data frame for the differential analysis result of proteins, returned by the function extractMeanDiff with the option perProtein=TRUE. The data frame contains columns of Protein, Label, log2FC, SE, Tvalue, DF, and pvalue.

Value

A data frame.

Examples

sim <- PTMsimulateExperiment(
    nGroup=2, nRep=2, nProtein=1, nSite=1, nFeature=5,
    logAbundance=list(
        PTM=list(mu=25, delta=c(0, 1), sRep=0.2, sPeak=0.05),
        PROTEIN=list(mu=25, delta=c(0, 1), sRep=0.2, sPeak=0.05)
    )
)
summarized <- PTMsummarize(sim)
estimates <- PTMestimate(summarized)
res <- extractMeanDiff(estimates[["PTM"]], "G_1", "G_2", FALSE)
res_prot <- extractMeanDiff(estimates[["PROTEIN"]], "G_1", "G_2", TRUE)
adjustProteinLevel(res, res_prot)
[Package MSstatsPTM version 1.0.0 Index]