Man pages for pulsedSilac
Analysis of pulsed-SILAC quantitative proteomics data
| addMisscleavedPeptides | Add miss-cleaved peptide expression levels for old isotope... |
| barplotCounts | Number of detected features per sample |
| barplotTimeCoverage | Number of detected features per sample |
| buildLinkerDf | Constructs a linkerDf that can be used as input when... |
| calculateAIC | Calculates the Akaike Information Criteria (AIC) |
| calculateIsotopeFraction | Calculates the incorporated isotope fraction |
| calculateIsotopeRatio | Ratio calculation |
| calculateOldIsotopePool | Estimates the fraction of old isotope for each time point |
| compareAIC | Calculates the probability of each model from a set of... |
| filterByMissingTimepoints | Filter proteins/peptides by the amount of measurements... |
| mefPE | SilacProteomicsExperiment with pulsed silac data from MEFs |
| merge | Merge |
| mergeModelsLists | Merge several models lists. |
| modelTurnover | Estimate protein/peptide turnover |
| mostStable | Most stable proteins/peptides |
| plotDistributionAssay | Distribution of assay data per condition and timepoint. |
| plotDistributionModel | Distribution of modelling output |
| plotIndividualModel | Fitted model(s) for a feature |
| recycleLightLysine | Data frame with miss cleaved peptides quantifications from... |
| scatterCompareAssays | Scatter plot of two conditions for each timepoint of an... |
| scatterCompareModels | Scatter plot of two conditions for a model metric. |
| SilacPeptideExperiment-class | SilacPeptideExperiment class |
| SilacPeptideExperiment-constructor | SilacPeptideExperiment constructor |
| SilacProteinExperiment-class | SilacProteinExperiment class |
| SilacProteinExperiment-constructor | SilacProteinExperiment constructor |
| SilacProteinPeptideExperiment-accessors | Accessors for the SilacProteinExperiment and... |
| SilacProteomicsExperiment-accessors | Accessors for the SilacProteomicsExperiment class |
| SilacProteomicsExperiment-class | SilacProteomicsExperiment class |
| SilacProteomicsExperiment-constructor | SilacProteomicsExperiment constructor |
| upsetTimeCoverage | Number of detected features per sample |
| wormsPE | ProteomicsExperiment with pulsed silac data from C. elegans... |
