$,SilacProteomicsExperiment-method	SilacProteomicsExperiment-accessors
$<-,SilacProteomicsExperiment-method	SilacProteomicsExperiment-accessors
.SilacPeptideExperiment	SilacPeptideExperiment-class
.SilacProteinExperiment	SilacProteinExperiment-class
.SilacProteomicsExperiment	SilacProteomicsExperiment-class
addMisscleavedPeptides	addMisscleavedPeptides
addMisscleavedPeptides,SilacPeptideExperiment-method	addMisscleavedPeptides
addMisscleavedPeptides,SilacProteinExperiment-method	addMisscleavedPeptides
addMisscleavedPeptides,SilacProteomicsExperiment-method	addMisscleavedPeptides
assayNames,SilacProteomicsExperiment-method	SilacProteomicsExperiment-accessors
assayNamesPept	SilacProteomicsExperiment-accessors
assayNamesPept,SilacPeptideExperiment-method	SilacProteomicsExperiment-accessors
assayNamesPept,SilacProteomicsExperiment-method	SilacProteomicsExperiment-accessors
assayNamesPept<-	SilacProteomicsExperiment-accessors
assayNamesPept<-,SilacPeptideExperiment-method	SilacProteomicsExperiment-accessors
assayNamesPept<-,SilacProteomicsExperiment-method	SilacProteomicsExperiment-accessors
assayNamesProt	SilacProteomicsExperiment-accessors
assayNamesProt,SilacProteinExperiment-method	SilacProteomicsExperiment-accessors
assayNamesProt,SilacProteomicsExperiment-method	SilacProteomicsExperiment-accessors
assayNamesProt<-	SilacProteomicsExperiment-accessors
assayNamesProt<-,SilacProteinExperiment-method	SilacProteomicsExperiment-accessors
assayNamesProt<-,SilacProteomicsExperiment-method	SilacProteomicsExperiment-accessors
assays	SilacProteomicsExperiment-accessors
assays,SilacProteomicsExperiment-method	SilacProteomicsExperiment-accessors
assays<-,SilacPeptideExperiment,ANY-method	SilacProteinPeptideExperiment-accessors
assays<-,SilacProteinExperiment,ANY-method	SilacProteinPeptideExperiment-accessors
assaysPept	SilacProteomicsExperiment-accessors
assaysPept,SilacPeptideExperiment-method	SilacProteomicsExperiment-accessors
assaysPept,SilacProteomicsExperiment-method	SilacProteomicsExperiment-accessors
assaysPept<-	SilacProteomicsExperiment-accessors
assaysPept<-,SilacPeptideExperiment-method	SilacProteomicsExperiment-accessors
assaysPept<-,SilacProteomicsExperiment-method	SilacProteomicsExperiment-accessors
assaysProt	SilacProteomicsExperiment-accessors
assaysProt,SilacProteinExperiment-method	SilacProteomicsExperiment-accessors
assaysProt,SilacProteomicsExperiment-method	SilacProteomicsExperiment-accessors
assaysProt<-	SilacProteomicsExperiment-accessors
assaysProt<-,SilacProteinExperiment-method	SilacProteomicsExperiment-accessors
assaysProt<-,SilacProteomicsExperiment-method	SilacProteomicsExperiment-accessors
barplotCounts	barplotCounts
barplotCounts,SilacPeptideExperiment-method	barplotCounts
barplotCounts,SilacProteinExperiment-method	barplotCounts
barplotCounts,SilacProteomicsExperiment-method	barplotCounts
barplotTimeCoverage	barplotTimeCoverage
barplotTimeCoverage,SilacPeptideExperiment-method	barplotTimeCoverage
barplotTimeCoverage,SilacProteinExperiment-method	barplotTimeCoverage
barplotTimeCoverage,SilacProteomicsExperiment-method	barplotTimeCoverage
buildLinkerDf	buildLinkerDf
calculateAIC	calculateAIC
calculateIsotopeFraction	calculateIsotopeFraction
calculateIsotopeFraction,SilacPeptideExperiment-method	calculateIsotopeFraction
calculateIsotopeFraction,SilacProteinExperiment-method	calculateIsotopeFraction
calculateIsotopeFraction,SilacProteomicsExperiment-method	calculateIsotopeFraction
calculateIsotopeRatio	calculateIsotopeRatio
calculateIsotopeRatio,SilacPeptideExperiment-method	calculateIsotopeRatio
calculateIsotopeRatio,SilacProteinExperiment-method	calculateIsotopeRatio
calculateIsotopeRatio,SilacProteomicsExperiment-method	calculateIsotopeRatio
calculateOldIsotopePool	calculateOldIsotopePool
calculateOldIsotopePool,SilacPeptideExperiment-method	calculateOldIsotopePool
calculateOldIsotopePool,SilacProteomicsExperiment-method	calculateOldIsotopePool
cbind,SilacPeptideExperiment-method	SilacProteinPeptideExperiment-accessors
cbind,SilacProteinExperiment-method	SilacProteinPeptideExperiment-accessors
cbind,SilacProteomicsExperiment-method	SilacProteomicsExperiment-accessors
coerce	SilacProteinPeptideExperiment-accessors
coerce,SilacProteinExperiment,data.frame-method	SilacProteinPeptideExperiment-accessors
coerce,SilacProteinExperiment,SummarizedExperiment-method	SilacProteinPeptideExperiment-accessors
colData,SilacProteomicsExperiment-method	SilacProteomicsExperiment-accessors
colData<-,SilacPeptideExperiment,ANY-method	SilacProteinPeptideExperiment-accessors
colData<-,SilacPeptideExperiment-method	SilacProteinPeptideExperiment-accessors
colData<-,SilacProteinExperiment,ANY-method	SilacProteinPeptideExperiment-accessors
colData<-,SilacProteinExperiment-method	SilacProteinPeptideExperiment-accessors
colData<-,SilacProteomicsExperiment,ANY-method	SilacProteomicsExperiment-accessors
colData<-,SilacProteomicsExperiment-method	SilacProteomicsExperiment-accessors
colnames,SilacProteomicsExperiment-method	SilacProteomicsExperiment-accessors
colnames<-,SilacProteomicsExperiment-method	SilacProteomicsExperiment-accessors
compareAIC	compareAIC
dim,SilacProteomicsExperiment-method	SilacProteomicsExperiment-accessors
filterByMissingTimepoints	filterByMissingTimepoints
filterByMissingTimepoints,SilacPeptideExperiment-method	filterByMissingTimepoints
filterByMissingTimepoints,SilacProteinExperiment-method	filterByMissingTimepoints
filterByMissingTimepoints,SilacProteomicsExperiment-method	filterByMissingTimepoints
length,SilacProteomicsExperiment-method	SilacProteomicsExperiment-accessors
linkerDf	SilacProteomicsExperiment-accessors
linkerDf,SilacProteomicsExperiment-method	SilacProteomicsExperiment-accessors
linkerDf<-	SilacProteomicsExperiment-accessors
linkerDf<-,SilacProteomicsExperiment-method	SilacProteomicsExperiment-accessors
mefPE	mefPE
merge	merge
merge,SilacPeptideExperiment,ANY-method	merge
merge,SilacProteinExperiment,ANY-method	merge
merge,SilacProteomicsExperiment,ANY-method	merge
mergeModelsLists	mergeModelsLists
metadata,SilacProteomicsExperiment-method	SilacProteomicsExperiment-accessors
metadata<-,SilacProteomicsExperiment-method	SilacProteomicsExperiment-accessors
metaoptions	SilacProteomicsExperiment-accessors
metaoptions,SilacPeptideExperiment-method	SilacProteinPeptideExperiment-accessors
metaoptions,SilacProteinExperiment-method	SilacProteinPeptideExperiment-accessors
metaoptions,SilacProteomicsExperiment-method	SilacProteomicsExperiment-accessors
metaoptions<-	SilacProteomicsExperiment-accessors
metaoptions<-,SilacPeptideExperiment-method	SilacProteinPeptideExperiment-accessors
metaoptions<-,SilacProteinExperiment-method	SilacProteinPeptideExperiment-accessors
metaoptions<-,SilacProteomicsExperiment-method	SilacProteomicsExperiment-accessors
modelTurnover	modelTurnover
modelTurnover,SilacPeptideExperiment-method	modelTurnover
modelTurnover,SilacProteinExperiment-method	modelTurnover
modelTurnover,SilacProteomicsExperiment-method	modelTurnover
mostStable	mostStable
mostStable,SilacPeptideExperiment-method	mostStable
mostStable,SilacProteinExperiment-method	mostStable
mostStable,SilacProteomicsExperiment-method	mostStable
ncol	SilacProteomicsExperiment-accessors
ncol,SilacProteomicsExperiment-method	SilacProteomicsExperiment-accessors
nrow,SilacProteomicsExperiment-method	SilacProteomicsExperiment-accessors
PeptExp	SilacProteomicsExperiment-accessors
plotDistributionAssay	plotDistributionAssay
plotDistributionAssay,SilacPeptideExperiment-method	plotDistributionAssay
plotDistributionAssay,SilacProteinExperiment-method	plotDistributionAssay
plotDistributionAssay,SilacProteomicsExperiment-method	plotDistributionAssay
plotDistributionModel	plotDistributionModel
plotIndividualModel	plotIndividualModel
plotIndividualModel,SilacPeptideExperiment-method	plotIndividualModel
plotIndividualModel,SilacProteinExperiment-method	plotIndividualModel
plotIndividualModel,SilacProteomicsExperiment-method	plotIndividualModel
ProtExp	SilacProteomicsExperiment-accessors
rbind,SilacPeptideExperiment-method	SilacProteinPeptideExperiment-accessors
rbind,SilacProteinExperiment-method	SilacProteinPeptideExperiment-accessors
rbind,SilacProteomicsExperiment-method	SilacProteomicsExperiment-accessors
recycleLightLysine	recycleLightLysine
rowData,SilacProteomicsExperiment-method	SilacProteomicsExperiment-accessors
rowData<-,SilacPeptideExperiment-method	SilacProteinPeptideExperiment-accessors
rowData<-,SilacProteinExperiment-method	SilacProteinPeptideExperiment-accessors
rowData<-,SilacProteomicsExperiment-method	SilacProteomicsExperiment-accessors
rowDataPept	SilacProteomicsExperiment-accessors
rowDataPept,SilacPeptideExperiment-method	SilacProteomicsExperiment-accessors
rowDataPept,SilacProteomicsExperiment-method	SilacProteomicsExperiment-accessors
rowDataPept<-	SilacProteomicsExperiment-accessors
rowDataPept<-,SilacPeptideExperiment-method	SilacProteomicsExperiment-accessors
rowDataPept<-,SilacProteomicsExperiment-method	SilacProteomicsExperiment-accessors
rowDataProt	SilacProteomicsExperiment-accessors
rowDataProt,SilacProteinExperiment-method	SilacProteomicsExperiment-accessors
rowDataProt,SilacProteomicsExperiment-method	SilacProteomicsExperiment-accessors
rowDataProt<-	SilacProteomicsExperiment-accessors
rowDataProt<-,SilacProteinExperiment-method	SilacProteomicsExperiment-accessors
rowDataProt<-,SilacProteomicsExperiment-method	SilacProteomicsExperiment-accessors
rownamesPept	SilacProteomicsExperiment-accessors
rownamesPept,SilacProteomicsExperiment-method	SilacProteomicsExperiment-accessors
rownamesPept<-	SilacProteomicsExperiment-accessors
rownamesPept<-,SilacProteomicsExperiment-method	SilacProteomicsExperiment-accessors
rownamesProt	SilacProteomicsExperiment-accessors
rownamesProt,SilacProteomicsExperiment-method	SilacProteomicsExperiment-accessors
rownamesProt<-	SilacProteomicsExperiment-accessors
rownamesProt<-,SilacProteomicsExperiment-method	SilacProteomicsExperiment-accessors
scatterCompareAssays	scatterCompareAssays
scatterCompareAssays,SilacPeptideExperiment-method	scatterCompareAssays
scatterCompareAssays,SilacProteinExperiment-method	scatterCompareAssays
scatterCompareAssays,SilacProteomicsExperiment-method	scatterCompareAssays
scatterCompareModels	scatterCompareModels
SilacPeptideExperiment	SilacPeptideExperiment-constructor
SilacPeptideExperiment-class	SilacPeptideExperiment-class
SilacPeptideExperiment-constructor	SilacPeptideExperiment-constructor
SilacProteinExperiment	SilacProteinExperiment-constructor
SilacProteinExperiment-class	SilacProteinExperiment-class
SilacProteinExperiment-constructor	SilacProteinExperiment-constructor
SilacProteinPeptideExperiment-accessors	SilacProteinPeptideExperiment-accessors
SilacProteomicsExperiment	SilacProteomicsExperiment-constructor
SilacProteomicsExperiment-accessors	SilacProteomicsExperiment-accessors
SilacProteomicsExperiment-class	SilacProteomicsExperiment-class
SilacProteomicsExperiment-constructor	SilacProteomicsExperiment-constructor
subset,SilacPeptideExperiment-method	SilacProteinPeptideExperiment-accessors
subset,SilacProteinExperiment-method	SilacProteinPeptideExperiment-accessors
subset,SilacProteomicsExperiment-method	SilacProteomicsExperiment-accessors
subsetPept	SilacProteomicsExperiment-accessors
subsetPept,SilacPeptideExperiment-method	SilacProteomicsExperiment-accessors
subsetPept,SilacProteomicsExperiment-method	SilacProteomicsExperiment-accessors
subsetProt	SilacProteomicsExperiment-accessors
subsetProt,SilacProteinExperiment-method	SilacProteomicsExperiment-accessors
subsetProt,SilacProteomicsExperiment-method	SilacProteomicsExperiment-accessors
upsetTimeCoverage	upsetTimeCoverage
upsetTimeCoverage,SilacPeptideExperiment-method	upsetTimeCoverage
upsetTimeCoverage,SilacProteinExperiment-method	upsetTimeCoverage
upsetTimeCoverage,SilacProteomicsExperiment-method	upsetTimeCoverage
wormsPE	wormsPE
[,SilacProteomicsExperiment,ANY,ANY,ANY-method	SilacProteomicsExperiment-accessors
[,SilacProteomicsExperiment-ANY-ANY-method	SilacProteomicsExperiment-accessors
