STATegRa: Classes and methods for multi-omics data integration

Classes and tools for multi-omics data integration.

Author
STATegra Consortia
Date of publication
None
Maintainer
David Gomez-Cabrero <david.gomezcabrero@ki.se>, Patricia Sebastián-León <psebastian@cipf.es>, Gordon Ball <gordon.ball@ki.se>
License
GPL-2
Version
1.8.0

View on Bioconductor

Man pages

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

Files in this package

STATegRa/DESCRIPTION
STATegRa/NAMESPACE
STATegRa/R
STATegRa/R/STATegRa_combiningMappings.R
STATegRa/R/STATegRa_fused.R
STATegRa/R/STATegRa_holistOmics.R
STATegRa/R/STATegRa_omicsCLUST_bioDist.R
STATegRa/R/STATegRa_omicsCLUST_bioDistW.R
STATegRa/R/STATegRa_omicsCLUST_bioMap.R
STATegRa/R/STATegRa_omicsNPC.R
STATegRa/R/STATegRa_omicsNPC_internal.R
STATegRa/R/STATegRa_omicsPCA_caClass.R
STATegRa/R/STATegRa_omicsPCA_methods.R
STATegRa/R/STATegRa_omicsPCA_plotting.R
STATegRa/R/STATegRa_package.R
STATegRa/build
STATegRa/build/vignette.rds
STATegRa/data
STATegRa/data/STATegRa_S1.rda
STATegRa/data/STATegRa_S2.rda
STATegRa/data/STATegRa_S3.rda
STATegRa/data/TCGA_BRCA_Batch_93.rda
STATegRa/data/datalist
STATegRa/inst
STATegRa/inst/NEWS
STATegRa/inst/doc
STATegRa/inst/doc/STATegRa.R
STATegRa/inst/doc/STATegRa.Rmd
STATegRa/inst/doc/STATegRa.html
STATegRa/inst/unitTests
STATegRa/inst/unitTests/test_PCA.selection.R
STATegRa/inst/unitTests/test_createOmicsExpressionSet.R
STATegRa/inst/unitTests/test_modelSelection.R
STATegRa/inst/unitTests/test_selectCommonComps.R
STATegRa/man
STATegRa/man/PCA.selection.Rd
STATegRa/man/STATegRa-deprecated.Rd
STATegRa/man/STATegRa.Rd
STATegRa/man/STATegRaUsersGuide.Rd
STATegRa/man/STATegRa_data.Rd
STATegRa/man/STATegRa_data_TCGA_BRCA.Rd
STATegRa/man/bioDist.Rd
STATegRa/man/bioDistFeature.Rd
STATegRa/man/bioDistFeaturePlot.Rd
STATegRa/man/bioDistW.Rd
STATegRa/man/bioDistWPlot.Rd
STATegRa/man/bioDistclass.Rd
STATegRa/man/bioMap.Rd
STATegRa/man/biplotRes.Rd
STATegRa/man/caClass-class.Rd
STATegRa/man/combiningMappings.Rd
STATegRa/man/createOmicsExpressionSet.Rd
STATegRa/man/getInitialData.Rd
STATegRa/man/getLoadings.Rd
STATegRa/man/getMethodInfo.Rd
STATegRa/man/getPreprocessing.Rd
STATegRa/man/getScores.Rd
STATegRa/man/getVAF.Rd
STATegRa/man/holistOmics.Rd
STATegRa/man/modelSelection.Rd
STATegRa/man/omicsCompAnalysis.Rd
STATegRa/man/omicsNPC.Rd
STATegRa/man/plotRes.Rd
STATegRa/man/plotVAF.Rd
STATegRa/man/selectCommonComps.Rd
STATegRa/tests
STATegRa/tests/STATEgRa_Example.omicsCLUST.R
STATegRa/tests/STATEgRa_Example.omicsPCA.R
STATegRa/tests/STATegRa_Example.omicsNPC.R
STATegRa/tests/runTests.R
STATegRa/vignettes
STATegRa/vignettes/STATegRa.Rmd
STATegRa/vignettes/bibliography.bib
STATegRa/vignettes/img
STATegRa/vignettes/img/omicsClustering.jpg
STATegRa/vignettes/img/omicsPCA.png