R: Simulate PTM quantification experiments

PTMsimulateExperiment {MSstatsPTM}

R Documentation

Simulate PTM quantification experiments

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)
    )
)

[Package MSstatsPTM version 1.0.0 Index]