addMisscleavedPeptides: Add miss-cleaved peptide expression levels for old isotope...

Description Usage Arguments Value Examples

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:

Non-detected measurements should be NA.

Usage

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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

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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')

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