MultiAssayExperiment: Create Classes and Functions for Managing Multiple Assays on Sets of Samples

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Develop an integrative environment where multiple assays are managed and preprocessed for genomic data analysis.

Author
MultiAssay SIG
Date of publication
None
Maintainer
Marcel Ramos <mramos09@gmail.com>
License
Artistic-2.0
Version
1.0.0

View on Bioconductor

Man pages

API
Refer to the API documentation
assay-RangedRaggedAssay-ANY-method
Create a Matrix of score values using a GRanges or own ranges
ExperimentList
experiment Acessor function for the 'ExperimentList' slot of...
ExperimentList-class
A container for multi-experiment data
experiments
Accessor function for the 'ExperimentList' slot of a...
experiments-set
Replace an 'ExperimentList' slot value with a given...
getHits
Find hits by class type
hasAssay
Checking assay method for any class
mapToList
Convert map from data.frame or DataFrame to list and vice...
MultiAssayExperiment
MultiAssayExperiment: Build an integrative multi-assay...
MultiAssayExperiment-class
An integrative MultiAssay class for experiment data
PrepMultiAssay
Prepare a 'MultiAssayExperiment' instance
RangedRaggedAssay
Create a RangedRaggedAssay
RangedRaggedAssay-class
An extension of the GRangesList class
sampleMap
Accessor function for the 'sampleMap' slot of a...
sampleMap-set
Replace a slot value with a given 'DataFrame'
subsetByAssay
Subset 'MultiAssayExperiment' object by Assay type
subsetByColumn
Subset 'MultiAssayExperiment' object
subsetByRow
Subset 'MultiAssayExperiment' object by Feature

Files in this package

MultiAssayExperiment/DESCRIPTION
MultiAssayExperiment/NAMESPACE
MultiAssayExperiment/R
MultiAssayExperiment/R/API.R
MultiAssayExperiment/R/ExperimentList-class.R
MultiAssayExperiment/R/MultiAssayExperiment-class.R
MultiAssayExperiment/R/MultiAssayExperiment-methods.R
MultiAssayExperiment/R/MultiAssayExperiment-pkg.R
MultiAssayExperiment/R/MultiAssayExperiment.R
MultiAssayExperiment/R/PrepMultiAssay.R
MultiAssayExperiment/R/RangedRaggedAssay-class.R
MultiAssayExperiment/R/assay-methods.R
MultiAssayExperiment/R/hasAssay.R
MultiAssayExperiment/R/listToMap.R
MultiAssayExperiment/R/mapToList.R
MultiAssayExperiment/README.md
MultiAssayExperiment/build
MultiAssayExperiment/build/vignette.rds
MultiAssayExperiment/inst
MultiAssayExperiment/inst/NEWS
MultiAssayExperiment/inst/doc
MultiAssayExperiment/inst/doc/MultiAssayExperiment.R
MultiAssayExperiment/inst/doc/MultiAssayExperiment.Rmd
MultiAssayExperiment/inst/doc/MultiAssayExperiment.html
MultiAssayExperiment/inst/doc/UsingHDF5Array.R
MultiAssayExperiment/inst/doc/UsingHDF5Array.Rmd
MultiAssayExperiment/inst/doc/UsingHDF5Array.html
MultiAssayExperiment/inst/doc/pradMAEO-RTCGAToolbox.R
MultiAssayExperiment/inst/doc/pradMAEO-RTCGAToolbox.Rmd
MultiAssayExperiment/inst/doc/pradMAEO-RTCGAToolbox.html
MultiAssayExperiment/inst/extdata
MultiAssayExperiment/inst/extdata/exMatrix.R
MultiAssayExperiment/inst/extdata/exMatrix.h5
MultiAssayExperiment/inst/scripts
MultiAssayExperiment/inst/scripts/ExperimentList-Ex.R
MultiAssayExperiment/inst/scripts/MultiAssayExperiment-Ex.R
MultiAssayExperiment/inst/scripts/RangedRaggedAssay-Ex.R
MultiAssayExperiment/inst/scripts/getHits-Ex.R
MultiAssayExperiment/inst/scripts/listToMap-Ex.R
MultiAssayExperiment/inst/scripts/sampleMap-Ex.R
MultiAssayExperiment/man
MultiAssayExperiment/man/API.Rd
MultiAssayExperiment/man/ExperimentList-class.Rd
MultiAssayExperiment/man/ExperimentList.Rd
MultiAssayExperiment/man/MultiAssayExperiment-class.Rd
MultiAssayExperiment/man/MultiAssayExperiment.Rd
MultiAssayExperiment/man/PrepMultiAssay.Rd
MultiAssayExperiment/man/RangedRaggedAssay-class.Rd
MultiAssayExperiment/man/RangedRaggedAssay.Rd
MultiAssayExperiment/man/assay-RangedRaggedAssay-ANY-method.Rd
MultiAssayExperiment/man/experiments-set.Rd
MultiAssayExperiment/man/experiments.Rd
MultiAssayExperiment/man/getHits.Rd
MultiAssayExperiment/man/hasAssay.Rd
MultiAssayExperiment/man/mapToList.Rd
MultiAssayExperiment/man/sampleMap-set.Rd
MultiAssayExperiment/man/sampleMap.Rd
MultiAssayExperiment/man/subsetByAssay.Rd
MultiAssayExperiment/man/subsetByColumn.Rd
MultiAssayExperiment/man/subsetByRow.Rd
MultiAssayExperiment/tests
MultiAssayExperiment/tests/testthat
MultiAssayExperiment/tests/testthat.R
MultiAssayExperiment/tests/testthat/test-ExperimentList-class.R
MultiAssayExperiment/tests/testthat/test-MultiAssayExperiment.R
MultiAssayExperiment/tests/testthat/test-colnameOrder.R
MultiAssayExperiment/tests/testthat/test-constructors.R
MultiAssayExperiment/tests/testthat/test-drop.R
MultiAssayExperiment/tests/testthat/test-emptybuilders.R
MultiAssayExperiment/tests/testthat/test-methods.R
MultiAssayExperiment/tests/testthat/test-rowcolnames.R
MultiAssayExperiment/tests/testthat/test-subset.R
MultiAssayExperiment/vignettes
MultiAssayExperiment/vignettes/MultiAssayExperiment.Rmd
MultiAssayExperiment/vignettes/UsingHDF5Array.Rmd
MultiAssayExperiment/vignettes/pradMAEO-RTCGAToolbox.Rmd