addMisscleavedPeptides {pulsedSilac} | R Documentation

## Add miss-cleaved peptide expression levels for old isotope recycling estimation

### Description

To estimate how much of the "old" isotope is being used in "new" proteins the expression level of miss-cleaved peptides that contain a mix of isotopes (one old and one new) and miss-cleaved peptides that contain only new isotopes can be used to estimate amino acid recycling. To add this information a `data.frame` with the following information is required:

- A column with ids that can be mapped to the peptide rowData (not necessary for `SilacProteinExperiment` objects).

- A column indicating which isotope configuration the peptide has: two heavy isotopes, mix of light and heavy isotope, etc.

- A set of columns with peptide expression quantification. The number of columns should be the same, and in the same order, as the number of samples in the `SilacProteinExperiment`, `SilacPeptideExperiment` or `SilacProteomicsExperiment`.

Non-detected measurements should be `NA`.

### Usage

    addMisscleavedPeptides(x, ...)

    ## S4 method for signature 'SilacProteinExperiment'
    addMisscleavedPeptides(x, newdata, modCol, dataCols, idColPept)

    ## S4 method for signature 'SilacPeptideExperiment'
    addMisscleavedPeptides(x, newdata, modCol, dataCols, idColPept)

    ## S4 method for signature 'SilacProteomicsExperiment'
    addMisscleavedPeptides(x, newdata, modCol, dataCols, idColPept)

### Arguments

`x` | A `SilacProteinExperiment`, `SilacPeptideExperiment` or `SilacProteomicsExperiment`.
`...` | Unused.
`newdata` | a `data.frame` containing the data described in the description.
`modCol` | `character` or `numeric` indicating which column of newdata contains the peptide's isotope configuration.
`dataCols` | `character` or `numeric` vector indicating which columns of newdata contain the quantitative data. It should have the same length as the number of samples in x (`ncol(x)`). Samples should be in the same order.
`idColPept` | `character` indicating which column contains the ids that will be used in the merge with rowDataPept(x). The column in newdata should have the same name as in rowDataPept(x).

### Value

A `SilacPeptideExperiment` or `SilacProteomicsExperiment` with new assay entries. If x is a `SilacProteinExperiment` then a `SilacPeptideExperiment` is returned.

### Examples

    data('wormsPE')
    data('recycleLightLysine')
    protPE <- ProtExp(wormsPE)
    missPE <- addMisscleavedPeptides(x = protPE,
                                     newdata = recycleLightLysine,
                                     idColPept = 'Sequence',
                                     modCol = 'Modifications',
                                     dataCols = c(18:31))

    names(assays(missPE))[1:2] <- c('int_lys8lys8', 'int_lys8lys0')
    missPE <- calculateOldIsotopePool(x = missPE, 'int_lys8lys8', 'int_lys8lys0')

    plotDistributionAssay(missPE, assayName = 'oldIsotopePool')

[Package pulsedSilac version 1.8.0 Index]