PTMcompareMeans {MSstatsPTM}R Documentation

Compare mean abundances for all PTM sites across conditions

Description

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

Usage

PTMcompareMeans(data, controls, cases, adjProtein = FALSE)

Arguments

data

A list of two elements named PTM and PROTEIN. The PTM list has four elements: protein (a string vector of protein names), site (a string vector of PTM sites), param (a list of model parameter estimates for each site), and df (a numeric vector of degrees of freedom for each model). The PROTEIN list includes all as in PTM, except the element site.

controls

A string vector of control groups in the comparisons.

cases

A string vector of case groups.

adjProtein

A logical. TRUE performs protein-level adjustment, FALSE otherwise. 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)
PTMcompareMeans(estimates, controls="G_1", cases="G_2")
[Package MSstatsPTM version 1.0.0 Index]