Analysis of pulsed-SILAC quantitative proteomics data


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Documentation for package ‘pulsedSilac’ version 1.0.1

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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