extractMeanDiff {MSstatsPTM}R Documentation

Compare mean abundances for PTM sites (or proteins) across conditions

Description

extractMeanDiff performs significance analysis for detection of changes in PTM mean abundances between conditions.

Usage

extractMeanDiff(data, controls, cases, perProtein = FALSE)

Arguments

data

A list of abundance estimates with the following elements: protein, site, param, and df. site may be excluded when performing per-protein analysis (perProtein is TRUE).

controls

A string vector of control groups in the comparisons.

cases

A string vector of case groups.

perProtein

A logical. TRUE ignores the site-level information for PTM and considers protein as a whole, FALSE performs site-level analysis. Default is FALSE.

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)
extractMeanDiff(estimates[["PTM"]], controls="G_1", cases="G_2", FALSE)
extractMeanDiff(estimates[["PROTEIN"]], controls="G_1", cases="G_2", TRUE)


[Package MSstatsPTM version 1.0.0 Index]