mostStable {pulsedSilac} | R Documentation

## Most stable proteins/peptides

### 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)

[Package pulsedSilac version 1.6.0 Index]