STATegRa: Classes and methods for multi-omics data integration

Classes and tools for multi-omics data integration.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("STATegRa")
AuthorSTATegra Consortia
Bioconductor views Clustering DimensionReduction PrincipalComponent Software StatisticalMethod
Date of publicationNone
MaintainerDavid Gomez-Cabrero <david.gomezcabrero@ki.se>, Patricia Sebastián-León <psebastian@cipf.es>, Gordon Ball <gordon.ball@ki.se>
LicenseGPL-2
Version1.8.0

View on Bioconductor

Functions

bioDist Man page
bioDist,character,character,bioMap,ExpressionSet,ExpressionSet-m Man page
bioDistclass Man page
bioDistFeature Man page
bioDistFeature,character,list,numeric-method Man page
bioDistFeaturePlot Man page
bioDistW Man page
bioDistW,character,list,matrix-method Man page
bioDistWPlot Man page
bioDistWPlot,character,list,character-method Man page
bioMap Man page
biplotRes Man page
biplotRes,caClass,character,numeric,character-method Man page
Block1 Man page
Block1.PCA Man page
Block2 Man page
Block2.PCA Man page
caClass-class Man page
combiningMappings Man page
createOmicsExpressionSet Man page
createOmicsExpressionSet,matrix-method Man page
ed Man page
ed.PCA Man page
getInitialData Man page
getInitialData,caClass-method Man page
getLoadings Man page
getLoadings,caClass-method Man page
getMethodInfo Man page
getMethodInfo,caClass-method Man page
getPreprocessing Man page
getPreprocessing,caClass-method Man page
getScores Man page
getScores,caClass-method Man page
getVAF Man page
getVAF,caClass-method Man page
holistOmics Man page
holistOmics,list,character-method Man page
mapdata Man page
modelSelection Man page
modelSelection,list,numeric,character-method Man page
omicsCompAnalysis Man page
omicsCompAnalysis,list,character,character,numeric,numeric-metho Man page
omicsNPC Man page
omicsNPC,list,data.frame-method Man page
omicsNPC,list,missing-method Man page
PCA.selection Man page
PCA.selection,matrix,character-method Man page
plotRes Man page
plotRes,caClass,numeric,character,character,logical,character-me Man page
plotVAF Man page
plotVAF,caClass-method Man page
selectCommonComps Man page
selectCommonComps,matrix,matrix,numeric-method Man page
STATegRa Man page
STATegRa_data Man page
STATegRa_data_TCGA_BRCA Man page
STATegRa-deprecated Man page
STATegRa-package Man page
STATegRaUsersGuide Man page
TCGA_BRCA_Data Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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