# Classes and methods for multi-omics data integration

## Documentation for package ‘STATegRa’ version 1.0.0

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

## Help Pages

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