Package: MultiDataSet 1.37.0

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Xavier Escribà Montagut

MultiDataSet: Implementation of MultiDataSet and ResultSet

Implementation of the BRGE's (Bioinformatic Research Group in Epidemiology from Center for Research in Environmental Epidemiology) MultiDataSet and ResultSet. MultiDataSet is designed for integrating multi omics data sets and ResultSet is a container for omics results. This package contains base classes for MEAL and rexposome packages.

Authors:Carlos Ruiz-Arenas [aut, cre], Carles Hernandez-Ferrer [aut], Juan R. Gonzalez [aut]

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MultiDataSet.pdf |MultiDataSet.html✨
MultiDataSet/json (API)
NEWS

# Install 'MultiDataSet' in R:
install.packages('MultiDataSet', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:
  • rset - Example 'ResultSet'

On BioConductor:MultiDataSet-1.39.0(bioc 3.23)MultiDataSet-1.38.0(bioc 3.22)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

softwaredatarepresentation

6.28 score 11 packages 28 scripts 2.1k downloads 5 mentions 26 exports 40 dependencies

Last updated from:f641cabdf0. Checks:1 ERROR, 7 WARNING, 2 OK. Indexed: yes.

TargetResultTotal timeArtifact
bioc-checksERROR385
linux-devel-x86_64WARNING480
source / vignettesOK525
linux-release-x86_64WARNING492
macos-release-arm64WARNING238
macos-oldrel-arm64WARNING347
windows-develWARNING372
windows-releaseWARNING340
windows-oldrelWARNING382
wasm-releaseOK366

Exports:add_esetadd_genexpadd_methyadd_rnaseqadd_rseadd_seadd_snpsadd_tableas.listchrNumToCharcommonIdscommonSamplescreate_resultsetcreateMultiDataSetgetAssociationlambdaClaytonmae2mdsmds2maeoptplotqq_plotrowRangesrowRangesElementsvolcano_plotw_iclusterplusw_mcia

Dependencies:abindBiobaseBiocGenericscalibratecliDelayedArrayfarvergenericsGenomicRangesggplot2ggrepelgluegtableIRangesisobandlabelinglatticelifecyclelimmaMASSMatrixMatrixGenericsmatrixStatsqqmanR6RColorBrewerRcpprlangS4ArraysS4VectorsS7scalesSeqinfoSparseArraystatmodSummarizedExperimentvctrsviridisLitewithrXVector

Adding a new type of data to MultiDataSet objects

Carles Hernandez-Ferrer, Carlos Ruiz-Arenas, Alba Beltran-Gomila, Juan R. González

Rendered fromMultiDataSet_Extending_Proteome.Rmdusingknitr::rmarkdownon Nov 23 2025.

Last update: 2021-10-07
Started: 2017-02-27

Introduction to MultiDataSet

| Center for Research in Environmental Epidemiology (CREAL), Barcelona, Spain | Bioinformatics Research Group in Epidemiology | (http://www.creal.cat/brge.htm)

Rendered fromMultiDataSet.Rmdusingknitr::rmarkdownon Nov 23 2025.

Last update: 2018-02-15
Started: 2017-02-21

Readme and manuals

Help Manual

Help pageTopics
Method to add an 'eSet' to 'MultiDataSet'.add_eset
Method to add an expression microarray dataset to 'MultiDataSet'.add_genexp
Method to add a slot of methylation to 'MultiDataSet'.add_methy
Method to add an expression RNA seq dataset to 'MultiDataSet'.add_rnaseq
Method to add a 'RangedSummarizedExperiment' to 'MultiDataSet'.add_rse
Method to add a 'SummarizedExperiment' to 'MultiDataSet'.add_se
Method to add a slot of SNPs to 'MultiDataSet'.add_snps
Method to add a 'matrix' to 'MultiDataSet'.add_table
Convert chr numbers to chr stringschrNumToChar
Get the name of the ids common to all datasetscommonIds
Method to select samples that are present in all datasets.commonSamples
Method to extrat feature result from a ResultSetgetAssociation
Lambda Calculation for a vector of P-ValueslambdaClayton
Convert a 'MultiAssayExperiment' to a 'MultiDataSet'mae2mds
Convert a 'MultiDataSet' to a 'MultiAssayExperiment'mds2mae
MultiDataSet: Implementation of the BRGE's basic classesMultiDataSet
MultiDataSet instancesadd_eset,MultiDataSet,eSet-method add_genexp,MultiDataSet,ExpressionSet-method add_methy,MultiDataSet,GenomicRatioSet-method add_rnaseq,MultiDataSet,ExpressionSet-method add_rse,MultiDataSet,RangedSummarizedExperiment-method add_se,MultiDataSet,SummarizedExperiment-method add_snps,MultiDataSet,SnpSet-method add_table,MultiDataSet,matrix-method as.list as.list,MultiDataSet-method assayData assayData,MultiDataSet-method commonIds,MultiDataSet-method commonSamples,MultiDataSet-method createMultiDataSet dims dims,MultiDataSet-method fData fData,MultiDataSet-method featureData featureData,MultiDataSet-method length length,MultiDataSet-method MultiDataSet-class MultiDataSet-methods MultiDataSet-methods, names names,MultiDataSet-method ncol ncol,MultiDataSet-method nrow nrow,MultiDataSet-method pData pData,MultiDataSet-method phenoData phenoData,MultiDataSet-method rowRanges rowRanges,MultiDataSet-method rowRangesElements,MultiDataSet-method sampleNames,MultiDataSet-method subset,MultiDataSet-method w_iclusterplus,MultiDataSet-method w_mcia,MultiDataSet-method [ [,MultiDataSet,ANY,ANY,ANY-method [[,MultiDataSet,ANY,ANY-method
Method to get the options sued to create the ResultSetopt
Function to draw a QQ Plot from a vector of numbersqq_plot
Class ResultSetcreate_resultset fData,ResultSet-method getAssociation,ResultSet-method length,ResultSet-method names,ResultSet-method opt,ResultSet-method plot,ResultSet,ANY-method ResultSet ResultSet-class ResultSet-methods varLabels,ResultSet-method
Get the name of the datasets that have rowRangesrowRangesElements
Example 'ResultSet'rset
Function to draw a Volcano Plotvolcano_plot
Apply iClusterPlus clustering method to a MultiDataSet objectw_iclusterplus
Apply mcia integration method to a MultiDataSet objectw_mcia
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