PTMsimulateExperiment: Simulate PTM quantification experiments

In MSstatsPTM: Statistical Characterization of Post-translational Modifications

Description

PTMsimulateExperiment simulates a PTM quantification experiment with a list of log2-intensities of multiple spectral features, PTM sites and the corresponding proteins, in multiple MS runs and conditions.

Usage

PTMsimulateExperiment(nGroup, nRep, nProtein, nSite, nFeature, logAbundance)

Arguments

nGroup	An integer to specify the number of conditions.
nRep	An integer to specify the number of replicates per condition.
nProtein	An integer to specify the number of protein.
nSite	An integer to specify the number of PTM sites per protein.
nFeature	An integer to specify the number of features per site.
logAbundance	A list of two lists named PTM and PROTEIN. Each contains four elements: mu (a numeric representing the overall mean log2-abundance), delta (a numeric vector for the deviation of the mean log2-abundance for each group from the overall mean), sRep (a numeric representing the standard deviation for run-to-run variation), and sPeak (a numeric representing the standard deviation in peak log2-intensities).

Value

A tibble with columns of protein, site, group, run, feature, log2inty.

Examples

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)
    )
)

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