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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 |