# Analysis of pulsed-SILAC quantitative proteomics data

## Documentation for package ‘pulsedSilac’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

A B C D F L M N P R S U W misc

## -- A --

addMisscleavedPeptides | Add miss-cleaved peptide expression levels for old isotope recycling estimation
addMisscleavedPeptides-method | Add miss-cleaved peptide expression levels for old isotope recycling estimation
assayNames-method | Accessors for the SilacProteomicsExperiment class
assayNamesPept | Accessors for the SilacProteomicsExperiment class
assayNamesPept-method | Accessors for the SilacProteomicsExperiment class
assayNamesPept<- | Accessors for the SilacProteomicsExperiment class
assayNamesPept<--method | Accessors for the SilacProteomicsExperiment class
assayNamesProt | Accessors for the SilacProteomicsExperiment class
assayNamesProt-method | Accessors for the SilacProteomicsExperiment class
assayNamesProt<- | Accessors for the SilacProteomicsExperiment class
assayNamesProt<--method | Accessors for the SilacProteomicsExperiment class
assays | Accessors for the SilacProteomicsExperiment class
assays-method | Accessors for the SilacProteomicsExperiment class
assays<--method | Accessors for the SilacProteinExperiment and SilacPeptideExperiment classes
assaysPept | Accessors for the SilacProteomicsExperiment class
assaysPept-method | Accessors for the SilacProteomicsExperiment class
assaysPept<- | Accessors for the SilacProteomicsExperiment class
assaysPept<--method | Accessors for the SilacProteomicsExperiment class
assaysProt | Accessors for the SilacProteomicsExperiment class
assaysProt-method | Accessors for the SilacProteomicsExperiment class
assaysProt<- | Accessors for the SilacProteomicsExperiment class
assaysProt<--method | Accessors for the SilacProteomicsExperiment class

## -- B --

barplotCounts | Number of detected features per sample
barplotCounts-method | Number of detected features per sample
barplotTimeCoverage | Number of detected features per sample
barplotTimeCoverage-method | Number of detected features per sample
buildLinkerDf | Constructs a linkerDf that can be used as input when constructing a SilacProteomicsExperiment

## -- C --

calculateAIC | Calculates the Akaike Information Criteria (AIC)
calculateIsotopeFraction | Calculates the incorporated isotope fraction
calculateIsotopeFraction-method | Calculates the incorporated isotope fraction
calculateIsotopeRatio | Ratio calculation
calculateIsotopeRatio-method | Ratio calculation
calculateOldIsotopePool | Estimates the fraction of old isotope for each time point
calculateOldIsotopePool-method | Estimates the fraction of old isotope for each time point
cbind-method | Accessors for the SilacProteinExperiment and SilacPeptideExperiment classes
cbind-method | Accessors for the SilacProteomicsExperiment class
coerce | Accessors for the SilacProteinExperiment and SilacPeptideExperiment classes
coerce-method | Accessors for the SilacProteinExperiment and SilacPeptideExperiment classes
colData-method | Accessors for the SilacProteomicsExperiment class
colData<--method | Accessors for the SilacProteinExperiment and SilacPeptideExperiment classes
colData<--method | Accessors for the SilacProteomicsExperiment class
colnames-method | Accessors for the SilacProteomicsExperiment class
colnames<--method | Accessors for the SilacProteomicsExperiment class
compareAIC | Calculates the probability of each model from a set of models.

## -- D --

dim-method | Accessors for the SilacProteomicsExperiment class

## -- F --

filterByMissingTimepoints | Filter proteins/peptides by the amount of measurements overtime
filterByMissingTimepoints-method | Filter proteins/peptides by the amount of measurements overtime

## -- L --

length-method | Accessors for the SilacProteomicsExperiment class
linkerDf | Accessors for the SilacProteomicsExperiment class
linkerDf-method | Accessors for the SilacProteomicsExperiment class
linkerDf<- | Accessors for the SilacProteomicsExperiment class
linkerDf<--method | Accessors for the SilacProteomicsExperiment class

## -- M --

mefPE | SilacProteomicsExperiment with pulsed silac data from MEFs
merge | Merge
merge-method | Merge
mergeModelsLists | Merge several models lists.
metadata-method | Accessors for the SilacProteomicsExperiment class
metadata<--method | Accessors for the SilacProteomicsExperiment class
metaoptions | Accessors for the SilacProteomicsExperiment class
metaoptions-method | Accessors for the SilacProteinExperiment and SilacPeptideExperiment classes
metaoptions-method | Accessors for the SilacProteomicsExperiment class
metaoptions<- | Accessors for the SilacProteomicsExperiment class
metaoptions<--method | Accessors for the SilacProteinExperiment and SilacPeptideExperiment classes
metaoptions<--method | Accessors for the SilacProteomicsExperiment class
modelTurnover | Estimate protein/peptide turnover
modelTurnover-method | Estimate protein/peptide turnover
mostStable | Most stable proteins/peptides
mostStable-method | Most stable proteins/peptides

## -- N --

ncol | Accessors for the SilacProteomicsExperiment class
ncol-method | Accessors for the SilacProteomicsExperiment class
nrow-method | Accessors for the SilacProteomicsExperiment class

## -- P --

PeptExp | Accessors for the SilacProteomicsExperiment class
plotDistributionAssay | Distribution of assay data per condition and timepoint.
plotDistributionAssay-method | Distribution of assay data per condition and timepoint.
plotDistributionModel | Distribution of modelling output
plotIndividualModel | Fitted model(s) for a feature
plotIndividualModel-method | Fitted model(s) for a feature
ProtExp | Accessors for the SilacProteomicsExperiment class

## -- R --

rbind-method | Accessors for the SilacProteinExperiment and SilacPeptideExperiment classes
rbind-method | Accessors for the SilacProteomicsExperiment class
recycleLightLysine | Data frame with miss cleaved peptides quantifications from MaxQuant
rowData-method | Accessors for the SilacProteomicsExperiment class
rowData<--method | Accessors for the SilacProteinExperiment and SilacPeptideExperiment classes
rowData<--method | Accessors for the SilacProteomicsExperiment class
rowDataPept | Accessors for the SilacProteomicsExperiment class
rowDataPept-method | Accessors for the SilacProteomicsExperiment class
rowDataPept<- | Accessors for the SilacProteomicsExperiment class
rowDataPept<--method | Accessors for the SilacProteomicsExperiment class
rowDataProt | Accessors for the SilacProteomicsExperiment class
rowDataProt-method | Accessors for the SilacProteomicsExperiment class
rowDataProt<- | Accessors for the SilacProteomicsExperiment class
rowDataProt<--method | Accessors for the SilacProteomicsExperiment class
rownamesPept | Accessors for the SilacProteomicsExperiment class
rownamesPept-method | Accessors for the SilacProteomicsExperiment class
rownamesPept<- | Accessors for the SilacProteomicsExperiment class
rownamesPept<--method | Accessors for the SilacProteomicsExperiment class
rownamesProt | Accessors for the SilacProteomicsExperiment class
rownamesProt-method | Accessors for the SilacProteomicsExperiment class
rownamesProt<- | Accessors for the SilacProteomicsExperiment class
rownamesProt<--method | Accessors for the SilacProteomicsExperiment class

## -- S --

scatterCompareAssays | Scatter plot of two conditions for each timepoint of an assay.
scatterCompareAssays-method | Scatter plot of two conditions for each timepoint of an assay.
scatterCompareModels | Scatter plot of two conditions for a model metric.
SilacPeptideExperiment | SilacPeptideExperiment constructor
SilacPeptideExperiment-class | SilacPeptideExperiment class
SilacPeptideExperiment-constructor | SilacPeptideExperiment constructor
SilacProteinExperiment | SilacProteinExperiment constructor
SilacProteinExperiment-class | SilacProteinExperiment class
SilacProteinExperiment-constructor | SilacProteinExperiment constructor
SilacProteinPeptideExperiment-accessors | Accessors for the SilacProteinExperiment and SilacPeptideExperiment classes
SilacProteomicsExperiment | SilacProteomicsExperiment constructor
SilacProteomicsExperiment-accessors | Accessors for the SilacProteomicsExperiment class
SilacProteomicsExperiment-class | SilacProteomicsExperiment class
SilacProteomicsExperiment-constructor | SilacProteomicsExperiment constructor
subset-method | Accessors for the SilacProteinExperiment and SilacPeptideExperiment classes
subset-method | Accessors for the SilacProteomicsExperiment class
subsetPept | Accessors for the SilacProteomicsExperiment class
subsetPept-method | Accessors for the SilacProteomicsExperiment class
subsetProt | Accessors for the SilacProteomicsExperiment class
subsetProt-method | Accessors for the SilacProteomicsExperiment class

## -- U --

upsetTimeCoverage | Number of detected features per sample
upsetTimeCoverage-method | Number of detected features per sample

## -- W --

wormsPE | ProteomicsExperiment with pulsed silac data from C. elegans strains

## -- misc --

$-method | Accessors for the SilacProteomicsExperiment class
$<--method | Accessors for the SilacProteomicsExperiment class
.SilacPeptideExperiment | SilacPeptideExperiment class
.SilacProteinExperiment | SilacProteinExperiment class
.SilacProteomicsExperiment | SilacProteomicsExperiment class
[-method | Accessors for the SilacProteomicsExperiment class