A DownStream Chemo-Proteomics Analysis Pipeline


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Documentation for package ‘Doscheda’ version 1.31.0

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doscheda-package Doscheda: A package for Down Stream Chemo-Proteomics Data Analysis
boxplot-method Default boxplot for objects of class ChemoProtSet
ChemoProtSet-class An S4 class to run the doscheda pipeline
corrPlot Plot showing correlation between all channels across replicates
corrPlot-method Plot showing correlation between all channels across replicates
densityPlot Density plot for objects of class ChemoProtSet
densityPlot-method Density plot for objects of class ChemoProtSet
doscheda Doscheda: A package for Down Stream Chemo-Proteomics Data Analysis
doschedaApp Run shiny application for DOSCHEDA
doschedaData Peptide Intensity data set for Doscheda
DoschedaSet An S4 class to run the doscheda pipeline
fitModel Method to fit a model to an object of class 'ChemoProtSet'
fitModel-method Method to fit a model to an object of class 'ChemoProtSet'
getDatasets Accessor function for the datasets slot.
getDatasets-method Accessor function for the datasets slot.
getFinal Accessor function for the finalData slot.
getFinal-method Accessor function for the finalData slot.
getInput Accessor function for the Input
getInput-method Accessor function for the Input
getNorm Accessor function for the normData
getNorm-method Accessor function for the normData
getParameters Accessor function for the parameters slot.
getParameters-method Accessor function for the parameters slot.
makeReport Create report from 'ChemProtSet' object
meanSdPlot MeanSd plot for objects of class ChemoProtSet
meanSdPlot-method MeanSd plot for objects of class ChemoProtSet
pcaPlot PCA of the main data sets contained in a object of class ChemoProtSet
pcaPlot-method PCA of the main data sets contained in a object of class ChemoProtSet
plot.ChemoProtSet Default plot for objects of class ChemoProtSet
processedExample Processed Peptide Intensity data set for Doscheda
removePeptides Method to remove peptides from input data of an object of class 'ChemoProtSet'
removePeptides-method Method to remove peptides from input data of an object of class 'ChemoProtSet'
replicatePlot Plot replicates between concentrations
replicatePlot-method Plot replicates between concentrations
runDoscheda Wrapper Function to run the entire Doscheda pipeline
runNormalisation Method to remove peptides from input data of an object of class 'ChemoProtSet'
runNormalisation-method Method to remove peptides from input data of an object of class 'ChemoProtSet'
setData Method for attaching and standardising data for objects of class 'ChemoProtSet'
setData-method Method for attaching and standardising data for objects of class 'ChemoProtSet'
setParameters Method to set parameters for a ChemoProtSet
setParameters-method Method to set parameters for a ChemoProtSet
volcanoPlot Volcano plot for objects of class ChemoProtSet
volcanoPlot-method Volcano plot for objects of class ChemoProtSet