PTMestimate: Estimate log2-abundances of PTM sites and proteins

In tsunghengtsai/MSstatsPTM: Statistical Characterization of Post-translational Modifications

Description

PTMestimate takes as input the summarized log2-intensities for each PTM site, performs statistical modeling for the abundance of the site, and returns the estimates of model parameters for all sites in all experimental conditions. If protein log2-intensities are availble, the same estimation procedure is applied to each protein as well.

Usage

PTMestimate(data, fctBatch = FALSE)

Arguments

data	A list of two data frames named PTM and PROTEIN. The PTM data frame includes columns of protein, site, group, run, log2inty, and possibly, batch. The PROTEIN data frame includes all columns as in PTM except site.
fctBatch	A logical defining the handling of batch effect for all data or two logicals for the PTM and PROTEIN (if provided) data separately. TRUE considers a fixed batch effect, FALSE otherwise. Default is FALSE.

Value

A list of two lists 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 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)
    )
)
s <- PTMsummarize(sim)
PTMestimate(s)

tsunghengtsai/MSstatsPTM documentation built on Oct. 4, 2020, 5:51 p.m.