PTMnormalize: Normalization of log2-intensities across MS runs

In MSstatsPTM: Statistical Characterization of Post-translational Modifications

Description

PTMnormalize normalizes log2-intensities of spectral features across MS runs using a reference, or by equalizing a chosen summary (the log2 intensity summation, median, or mean of log2-intensities) from all features, features of modified peptides or features of unmodified peptides.

Usage

PTMnormalize(data, method = "median", refs)

Arguments

data	A list of two data frames named PTM and PROTEIN. Both the PTM data frame and the PROTEIN data frame include columns of run, feature, and log2inty.
method	A string defining the normalization method. Default is "median", which equalizes the medians of log2-intensities across MS runs. Other methods include to equalize log2 of intensity summation ("logsum"), to equalize the means of log2-intensities ("mean"), and to adjust the log2-intensities based on a reference ("ref") given by (refs).
refs	A list of two data frames named PTM and PROTEIN. Each defines the adjustment of log2-intensities for the MS runs in its corresponding data.

Value

Normalized data stored as in data.

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)
    )
)
PTMnormalize(sim)

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