PTMsummarize: Site-level summarization

In MSstatsPTM: Statistical Characterization of Post-translational Modifications

Description

PTMsummarize summarizes the peak log2-intensities for each PTM site into one value per run. If protein peak-intensities are availble, the same summarization procedure is applied to each protein as well.

Usage

PTMsummarize(data, method = "tmp")

Arguments

data	A list of two data frames named PTM and PROTEIN. The PTM data frame includes columns of protein, site, group, run, feature, log2inty, and possibly, batch. The PROTEIN data frame includes all columns as in PTM except site.
method	A string defining the summarization method. Default is "tmp", which applies Tukey's median polish. Other methods include log2 of the summation of peak intensities ("logsum"), and mean ("mean"), median ("median") and max ("max") of the log2-intensities.

Value

A list of two data frames named PTM and PROTEIN. The PTM data frame has columns of protein, site, group, run, log2inty, and possibly, batch. The PROTEIN data frame includes all as in PTM, except site.

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)
    )
)
PTMsummarize(sim)

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