MultiDataSet: Implementation of the BRGE's (Bioinformatic Research Group in Epidemiology from Center for Research in Environmental Epidemiology) MultiDataSet and MethylationSet

Implementation of the BRGE's (Bioinformatic Research Group in Epidemiology from Center for Research in Environmental Epidemiology) MultiDataSet and MethylationSet. MultiDataSet is designed for integrating multi omics data sets and MethylationSet to contain normalized methylation data. These package contains base classes for MEAL and rexposome packages.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("MultiDataSet")
AuthorCarlos Ruiz-Arenas [aut, cre], Carles Hernandez-Ferrer [aut], Juan R. Gonzalez [aut]
Bioconductor views DataRepresentation Software
Date of publicationNone
MaintainerCarlos Ruiz-Arenas <carlos.ruiz@isglobal.org>
Licensefile LICENSE
Version1.4.0

View on Bioconductor

Functions

[ Man page
add_eset Man page
add_eset,MultiDataSet,eSet-method Man page
add_genexp Man page
add_genexp,MultiDataSet,ExpressionSet-method Man page
add_methy Man page
add_methy,MultiDataSet,MethylationSet-method Man page
add_methy,MultiDataSet,RatioSet-method Man page
add_rnaseq Man page
add_rnaseq,MultiDataSet,ExpressionSet-method Man page
add_rse Man page
add_rse,MultiDataSet,RangedSummarizedExperiment-method Man page
add_se Man page
add_se,MultiDataSet,SummarizedExperiment-method Man page
add_snps Man page
add_snps,MultiDataSet,SnpSet-method Man page
add_table Man page
add_table,MultiDataSet,matrix-method Man page
as.list Man page
as.list,MultiDataSet-method Man page
assayData Man page
assayData,MultiDataSet-method Man page
betas Man page
betas,MethylationSet-method Man page
checkProbes Man page
checkProbes,MethylationSet-method Man page
checkSamples Man page
checkSamples,MethylationSet-method Man page
chrNumToChar Man page
commonIds Man page
commonIds,MultiDataSet-method Man page
commonSamples Man page
commonSamples,MultiDataSet-method Man page
createMultiDataSet Man page
dims Man page
dims,MultiDataSet-method Man page
fData Man page
fData,MultiDataSet-method Man page
featureData Man page
featureData,MultiDataSet-method Man page
getMs Man page
getMs,MethylationSet-method Man page
length Man page
length,MultiDataSet-method Man page
mae2mds Man page
mds2mae Man page
methylationSet Man page
MethylationSet Man page
MethylationSet Man page
MethylationSet-class Man page
MethylationSet-methods Man page
MethylationSet-methods Man page
MethylationSet-methods Man page
MethylationSet-methods Man page
MethylationSet-methods Man page
MethylationSet-methods Man page
MultiDataSet Man page
[,MultiDataSet,ANY,ANY,ANY-method Man page
[[,MultiDataSet,ANY,ANY-method Man page
MultiDataSet-class Man page
MultiDataSet-methods Man page
MultiDataSet-methods Man page
MultiDataSet-methods Man page
MultiDataSet-methods Man page
MultiDataSet-methods Man page
MultiDataSet-methods Man page
MultiDataSet-methods Man page
MultiDataSet-methods Man page
MultiDataSet-methods Man page
MultiDataSet-methods Man page
MultiDataSet-methods Man page
MultiDataSet-methods Man page
MultiDataSet-methods Man page
MultiDataSet-methods Man page
MultiDataSet-methods Man page
MultiDataSet-methods Man page
MultiDataSet-methods Man page
MultiDataSet-methods Man page
MultiDataSet-methods Man page
MultiDataSet-methods, Man page
MultiDataSet-package Man page
names Man page
names,MultiDataSet-method Man page
ncols Man page
ncols,MultiDataSet-method Man page
nrows Man page
nrows,MultiDataSet-method Man page
pData Man page
pData,MultiDataSet-method Man page
phenoData Man page
phenoData,MultiDataSet-method Man page
rowRanges Man page
rowRangesElements Man page
rowRangesElements,MultiDataSet-method Man page
rowRanges,MultiDataSet-method Man page
sampleNames,MultiDataSet-method Man page
subset,MultiDataSet-method Man page
w_iclusterplus Man page
w_iclusterplus,MultiDataSet-method Man page
w_mcia Man page
w_mcia,MultiDataSet-method Man page

Files

DESCRIPTION
LICENSE
NAMESPACE
NEWS
R
R/0_AllClasses.R R/1_AllGenerics.R R/MethylationSet_Constructor.R R/MethylationSet_Initializer.R R/MethylationSet_SettersGetters.R R/MethylationSet_Validator.R R/MethylationSet_checkProbes.R R/MethylationSet_checkSamples.R R/MethylationSet_show.R R/MultiDataSet-add_eset.R R/MultiDataSet-add_genexp.R R/MultiDataSet-add_methy.R R/MultiDataSet-add_rse.R R/MultiDataSet-add_se.R R/MultiDataSet-add_snps.R R/MultiDataSet-add_table.R R/MultiDataSet-as_list.R R/MultiDataSet-commonIds.R R/MultiDataSet-commonSamples.R R/MultiDataSet-constructor.R R/MultiDataSet-dims.R R/MultiDataSet-iclusterplus.R R/MultiDataSet-length.R R/MultiDataSet-mcia.R R/MultiDataSet-names.R R/MultiDataSet-ncols.R R/MultiDataSet-nrows.R R/MultiDataSet-rowRangesElements.R R/MultiDataSet-sampleNames.R R/MultiDataSet-show.R R/MultiDataSet.R R/MultiDataset-assayData.R R/MultiDataset-fData.R R/MultiDataset-pData.R R/MultiDataset-rowRanges.R R/MultiDataset-subseting.R R/chrNumToChar.R R/conversionFunctions.R R/downloadGEO.R
build
build/vignette.rds
inst
inst/CITATION
inst/doc
inst/doc/MultiDataSet.R
inst/doc/MultiDataSet.Rmd
inst/doc/MultiDataSet.html
inst/doc/MultiDataSet_Extending_Proteome.R
inst/doc/MultiDataSet_Extending_Proteome.Rmd
inst/doc/MultiDataSet_Extending_Proteome.html
inst/doc/MultiDataSet_Integration_Development.R
inst/doc/MultiDataSet_Integration_Development.Rmd
inst/doc/MultiDataSet_Integration_Development.html
man
man/MethylationSet-class.Rd man/MultiDataSet-class.Rd man/MultiDataSet.Rd man/add_eset.Rd man/add_genexp.Rd man/add_methy.Rd man/add_rnaseq-methods.Rd man/add_rse.Rd man/add_se.Rd man/add_snps.Rd man/add_table.Rd man/checkProbes-methods.Rd man/checkSamples-methods.Rd man/chrNumToChar.Rd man/commonIds.Rd man/commonSamples.Rd man/getMs-methods.Rd man/mae2mds.Rd man/mds2mae.Rd man/rowRangesElements.Rd man/w_iclusterplus.Rd man/w_mcia.Rd
tests
tests/testthat
tests/testthat.R tests/testthat/test_01addeSet.R tests/testthat/test_02addrse.R tests/testthat/test_03subsetting.R tests/testthat/test_04conversions.R tests/testthat/test_05addTable.R
vignettes
vignettes/IntegrationRefs.bib
vignettes/MultiDataSet.Rmd
vignettes/MultiDataSet_3party_Integration.Rmd
vignettes/MultiDataSet_Extending_Proteome.Rmd
vignettes/MultiDataSet_Integration_Development.Rmd

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