addMisscleavedPeptides {pulsedSilac} | R Documentation |
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
.
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)
x |
A |
... |
Unused. |
newdata |
a |
modCol |
|
dataCols |
|
idColPept |
|
A SilacPeptideExperiment
or SilacProteomicsExperiment
with new assay entries. If x is a SilacProteinExperiment
then a
SilacPeptideExperiment
is returned.
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')