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 |