# Classes and methods for multi-omics data integration

## Documentation for package ‘STATegRa’ version 1.10.0

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

## Help Pages

STATegRa-package | STATegRa
bioDist | bioDist
bioDist-method | bioDist
bioDistclass | bioDistclass
bioDistFeature | bioDistFeature
bioDistFeature-method | bioDistFeature
bioDistFeaturePlot | bioDistFeaturePlot
bioDistW | bioDistW
bioDistW-method | bioDistW
bioDistWPlot | bioDistWPlot
bioDistWPlot-method | bioDistWPlot
bioMap | bioMap
biplotRes | Biplot of component analysis
biplotRes-method | Biplot of component analysis
Block1 | STATegRa data
Block1.PCA | STATegRa data
Block2 | STATegRa data
Block2.PCA | STATegRa data
caClass-class | caClass
combiningMappings | combiningMappings, combining several mappings for use in the omicsNPC function
createOmicsExpressionSet | createOmicsExpressionSet
createOmicsExpressionSet-method | createOmicsExpressionSet
ed | STATegRa data
ed.PCA | STATegRa data
getInitialData | Retrieve initial data from caClass objects
getInitialData-method | Retrieve initial data from caClass objects
getLoadings | Retrieve component analysis loadings
getLoadings-method | Retrieve component analysis loadings
getMethodInfo | Retrieve information about component analysis method
getMethodInfo-method | Retrieve information about component analysis method
getPreprocessing | Retrieve information about preprocessing
getPreprocessing-method | Retrieve information about preprocessing
getScores | Retrieve component analysis scores
getScores-method | Retrieve component analysis scores
getVAF | Retrieve information abotut VAF
getVAF-method | Retrieve information abotut VAF
holistOmics | HolistOmics an application of NPC on omics datasets
holistOmics-method | HolistOmics an application of NPC on omics datasets
mapdata | STATegRa data
modelSelection | Find optimal common and distinctive components
modelSelection-method | Find optimal common and distinctive components
omicsCompAnalysis | Components analysis for multiple objects
omicsCompAnalysis-method | Components analysis for multiple objects
omicsNPC | omicsNPC, applying the Non-Parametric Combination (NPC) on omics datasets
omicsNPC-method | omicsNPC, applying the Non-Parametric Combination (NPC) on omics datasets
PCA.selection | Select an optimal number of components using PCA
PCA.selection-method | Select an optimal number of components using PCA
plotRes | Plot component analysis results
plotRes-method | Plot component analysis results
plotVAF | Plot VAF (Variance Explained For) from Component Analysis
plotVAF-method | Plot VAF (Variance Explained For) from Component Analysis
selectCommonComps | Select common components in two data blocks
selectCommonComps-method | Select common components in two data blocks
STATegRa | STATegRa
STATegRa-defunct | Defunct functions in STATegRa
STATegRaUsersGuide | STATegRaUsersGuide
STATegRa_data | STATegRa data
STATegRa_data_TCGA_BRCA | STATegRa data
TCGA_BRCA_Data | STATegRa data