mostStable: Most stable proteins/peptides

In marcpaga/pulsedSilac: Analysis of pulsed-SILAC quantitative proteomics data

Description

Finds which are the most stable proteins/peptides across the entire experiment. These proteins/peptides can be used to estimate the cell growth of each condition.

Usage

mostStable(x, ...)

## S4 method for signature 'SilacProteinExperiment'
mostStable(x, assayName, n, conditionCol)

## S4 method for signature 'SilacPeptideExperiment'
mostStable(x, assayName, n, conditionCol)

## S4 method for signature 'SilacProteomicsExperiment'
mostStable(x, assayName, n, mode, conditionCol)

Arguments

x	A SilacProteinExperiment, SilacPeptideExperiment or a SilacProteomicsExperiment object.
...	Unused.
assayName	Name of the assay to use.
n	A numeric indicating how many proteins should be returned.
conditionCol	A character, which indicates the column name in colData(x) that defines the different experiment conditions.
mode	A character indicating which level of data to use, either "protein" or "peptide". Only relevant for ProteomicsExperiment inputs.

Details

Proteins/peptides that are not found in all timepoints and in all conditions are not considered. The stability is based on ranking heavy label incorporation for each timepoint; therefore, lower values are correlated to higher stability.

Value

A SilacProteinExperiment, SilacPeptideExperiment or a SilacProteomicsExperiment object with the n most stable proteins/peptides.

Examples

data('mefPE')
mostStable(mefPE, assayName = 'fraction', n = 50)

marcpaga/pulsedSilac documentation built on March 11, 2020, 8:49 p.m.