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

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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.

Author
Carlos Ruiz-Arenas [aut, cre], Carles Hernandez-Ferrer [aut], Juan R. Gonz<c3><a1>lez [aut]
Date of publication
None
Maintainer
Carlos Ruiz-Arenas <carlos.ruiz@isglobal.org>
License
file LICENSE
Version
1.2.0

View on Bioconductor

Man pages

add_eset
Method to add an 'eSet' to 'MultiDataSet'.
add_genexp
Method to add an expression microarray dataset to...
add_methy
Method to add a slot of methylation to 'MultiDataSet'.
add_rnaseq-methods
Method to add an expression RNA seq dataset to...
add_rse
Method to add a 'RangedSummarizedExperiment' to...
add_snps
Method to add a slot of SNPs to 'MultiDataSet'.
checkProbes-methods
Filter 'MethylationSet' probes
checkSamples-methods
Modify a 'MethylationSet' to only contain common samples
chrNumToChar
Convert chr numbers to chr strings
commonIds
Get the name of the ids common to all datasets
commonSamples
Method to select samples that are present in all datasets.
getMs-methods
Transforms beta values to M-values
MethylationSet-class
MethylationSet instances
MultiDataSet
MultiDataSet: Implementation of the BRGE's basic classes
MultiDataSet-class
MultiDataSet instances
prepareMethylationSet
Generating a 'MethylationSet'
rowRangesElements
Get the name of the datasets that have rowRanges
w_iclusterplus
Apply iClusterPlus clustering method to a MultiDataSet object
w_mcia
Apply mcia integration method to a MultiDataSet object

Files in this package

MultiDataSet/DESCRIPTION
MultiDataSet/LICENSE
MultiDataSet/NAMESPACE
MultiDataSet/NEWS
MultiDataSet/R
MultiDataSet/R/0_AllClasses.R
MultiDataSet/R/1_AllGenerics.R
MultiDataSet/R/MethylationSet_Constructor.R
MultiDataSet/R/MethylationSet_Initializer.R
MultiDataSet/R/MethylationSet_SettersGetters.R
MultiDataSet/R/MethylationSet_Validator.R
MultiDataSet/R/MethylationSet_checkProbes.R
MultiDataSet/R/MethylationSet_checkSamples.R
MultiDataSet/R/MethylationSet_show.R
MultiDataSet/R/MultiDataSet-add_eset.R
MultiDataSet/R/MultiDataSet-add_genexp.R
MultiDataSet/R/MultiDataSet-add_methy.R
MultiDataSet/R/MultiDataSet-add_rse.R
MultiDataSet/R/MultiDataSet-add_snps.R
MultiDataSet/R/MultiDataSet-as_list.R
MultiDataSet/R/MultiDataSet-assayData.R
MultiDataSet/R/MultiDataSet-commonIds.R
MultiDataSet/R/MultiDataSet-commonSamples.R
MultiDataSet/R/MultiDataSet-constructor.R
MultiDataSet/R/MultiDataSet-fData.R
MultiDataSet/R/MultiDataSet-iclusterplus.R
MultiDataSet/R/MultiDataSet-length.R
MultiDataSet/R/MultiDataSet-mcia.R
MultiDataSet/R/MultiDataSet-names.R
MultiDataSet/R/MultiDataSet-rowRangesElements.R
MultiDataSet/R/MultiDataSet-sampleNames.R
MultiDataSet/R/MultiDataSet-show.R
MultiDataSet/R/MultiDataSet.R
MultiDataSet/R/MultiDataset-pData.R
MultiDataSet/R/MultiDataset-rowRanges.R
MultiDataSet/R/MultiDataset-subseting.R
MultiDataSet/R/chrNumToChar.R
MultiDataSet/R/downloadGEO.R
MultiDataSet/R/prepareMethylationSet.R
MultiDataSet/build
MultiDataSet/build/vignette.rds
MultiDataSet/inst
MultiDataSet/inst/doc
MultiDataSet/inst/doc/MultiDataSet.R
MultiDataSet/inst/doc/MultiDataSet.Rmd
MultiDataSet/inst/doc/MultiDataSet.html
MultiDataSet/man
MultiDataSet/man/MethylationSet-class.Rd
MultiDataSet/man/MultiDataSet-class.Rd
MultiDataSet/man/MultiDataSet.Rd
MultiDataSet/man/add_eset.Rd
MultiDataSet/man/add_genexp.Rd
MultiDataSet/man/add_methy.Rd
MultiDataSet/man/add_rnaseq-methods.Rd
MultiDataSet/man/add_rse.Rd
MultiDataSet/man/add_snps.Rd
MultiDataSet/man/checkProbes-methods.Rd
MultiDataSet/man/checkSamples-methods.Rd
MultiDataSet/man/chrNumToChar.Rd
MultiDataSet/man/commonIds.Rd
MultiDataSet/man/commonSamples.Rd
MultiDataSet/man/getMs-methods.Rd
MultiDataSet/man/prepareMethylationSet.Rd
MultiDataSet/man/rowRangesElements.Rd
MultiDataSet/man/w_iclusterplus.Rd
MultiDataSet/man/w_mcia.Rd
MultiDataSet/tests
MultiDataSet/tests/testthat
MultiDataSet/tests/testthat.R
MultiDataSet/tests/testthat/test_00createSet.R
MultiDataSet/tests/testthat/test_01addeSet.R
MultiDataSet/tests/testthat/test_02addrse.R
MultiDataSet/tests/testthat/test_03subsetting.R
MultiDataSet/vignettes
MultiDataSet/vignettes/MultiDataSet.Rmd