extractMeanDiff: Compare mean abundances for PTM sites (or proteins) across...

In MSstatsPTM: Statistical Characterization of Post-translational Modifications

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)

MSstatsPTM documentation built on Nov. 8, 2020, 5:49 p.m.