A B C D F L M N P R S U W misc
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 |
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 |
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. |
dim-method | Accessors for the SilacProteomicsExperiment class |
filterByMissingTimepoints | Filter proteins/peptides by the amount of measurements overtime |
filterByMissingTimepoints-method | Filter proteins/peptides by the amount of measurements overtime |
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 |
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 |
ncol | Accessors for the SilacProteomicsExperiment class |
ncol-method | Accessors for the SilacProteomicsExperiment class |
nrow-method | Accessors for the SilacProteomicsExperiment class |
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 |
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 |
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 |
upsetTimeCoverage | Number of detected features per sample |
upsetTimeCoverage-method | Number of detected features per sample |
wormsPE | ProteomicsExperiment with pulsed silac data from C. elegans strains |
$-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 |