Classes and methods for multi-omics data integration


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Documentation for package ‘STATegRa’ version 1.0.0

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STATegRa-package STATegRa
bioDist bioDist
bioDist-method bioDist
bioDistclass bioDistclass
bioDistclass-class bioDistclass
bioDistclass-constructor bioDistclass
bioDistFeature bioDistFeature
bioDistFeature-method bioDistFeature
bioDistFeaturePlot bioDistFeaturePlot
bioDistW bioDistW
bioDistW-method bioDistW
bioDistWPlot bioDistWPlot
bioDistWPlot-method bioDistWPlot
bioMap bioMap constructor
bioMap-class bioMap class
bioMap-constructor bioMap constructor
biplotRes Biplot results of Components Analysis
biplotRes-method Biplot results of Components Analysis
Block1 STATegRa_initial_data
Block1.PCA STATegRa_initial_data
Block2 STATegRa_initial_data
Block2.PCA STATegRa_initial_data
caClass-class caClass
class:bioDistclass bioDistclass
class:bioMap bioMap class
class:caClass caClass
createOmicsExpressionSet Create an ExpressionSet object since omics dataset.
createOmicsExpressionSet-method Create an ExpressionSet object since omics dataset.
ed STATegRa_initial_data
ed.PCA STATegRa_initial_data
getInitialData Retrieve Initial data from caClass objects
getInitialData-method Retrieve Initial data from caClass objects
getLoadings Retrieve information about the loadings obtained using 'omicsCompAnalysis' from an 'caClass-class'
getLoadings-method Retrieve information about the loadings obtained using 'omicsCompAnalysis' from an 'caClass-class'
getMethodInfo Retrieve information about the components analysis done using 'omicsCompAnalysis' from an 'caClass-class'
getMethodInfo-method Retrieve information about the components analysis done using 'omicsCompAnalysis' from an 'caClass-class'
getPreprocessing Retrieve information about the preprocessing done in 'omicsCompAnalysis' from an 'caClass-class'
getPreprocessing-method Retrieve information about the preprocessing done in 'omicsCompAnalysis' from an 'caClass-class'
getScores Retrieve information about the scores obtained using 'omicsCompAnalysis' from an 'caClass-class'
getScores-method Retrieve information about the scores obtained using 'omicsCompAnalysis' from an 'caClass-class'
getVAF Retrieve information about the VAF obtained using 'omicsCompAnalysis' from an 'caClass-class'
getVAF-method Retrieve information about the VAF obtained using 'omicsCompAnalysis' from an 'caClass-class'
mapdata STATegRa_initial_data
modelSelection Number of optimal common and distinctive components in object-wise data
modelSelection-method Number of optimal common and distinctive components in object-wise data
omicsCompAnalysis Components analysis for the analysis of object wise data
omicsCompAnalysis-method Components analysis for the analysis of object wise data
PCA.selection Selection of optimal number of components using PCA
PCA.selection-method Selection of optimal number of components using PCA
plotRes Plot results of Components Analysis
plotRes-method Plot results of Components Analysis
plotVAF Function to plot the VAF (Variance Explained For) obtained from Component Analysis.
plotVAF-method Function to plot the VAF (Variance Explained For) obtained from Component Analysis.
selectCommonComps Select common components of two blocks of object wise omics data.
selectCommonComps-method Select common components of two blocks of object wise omics data.
STATegRa STATegRa
STATegRaUsersGuide View STATegRa User's Guide
STATegRa_initial_data STATegRa_initial_data