Package: MultiDataSet 1.33.0

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'))

Peer review:

Datasets:
  • rset - Example 'ResultSet'

On BioConductor:MultiDataSet-1.33.0(bioc 3.20)MultiDataSet-1.32.0(bioc 3.19)

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

softwaredatarepresentation

26 exports 6.49 score 59 dependencies 11 dependents 5 mentions 28 scripts 1.7k downloads

Last updated 5 months agofrom:6edc287bf9. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 25 2024
R-4.5-winWARNINGSep 25 2024
R-4.5-linuxWARNINGSep 25 2024
R-4.4-winWARNINGSep 25 2024
R-4.4-macWARNINGSep 25 2024
R-4.3-winWARNINGSep 25 2024
R-4.3-macWARNINGSep 25 2024

Exports:add_esetadd_genexpadd_methyadd_rnaseqadd_rseadd_seadd_snpsadd_tableas.listchrNumToCharcommonIdscommonSamplescreate_resultsetcreateMultiDataSetgetAssociationlambdaClaytonmae2mdsmds2maeoptplotqq_plotrowRangesrowRangesElementsvolcano_plotw_iclusterplusw_mcia

Dependencies:abindaskpassBiobaseBiocGenericscalibrateclicolorspacecrayoncurlDelayedArrayfansifarverGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2ggrepelgluegtablehttrIRangesisobandjsonlitelabelinglatticelifecyclelimmamagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpillarpkgconfigqqmanR6RColorBrewerRcpprlangS4ArraysS4VectorsscalesSparseArraystatmodSummarizedExperimentsystibbleUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc

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 Sep 25 2024.

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 Sep 25 2024.

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