# A DownStream Chemo-Proteomics Analysis Pipeline

## Documentation for package ‘Doscheda’ version 1.35.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

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