MultiAssayExperiment: Software for the integration of multi-omics experiments in Bioconductor
Version 1.2.1

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

Browse man pages Browse package API and functions Browse package files

AuthorMultiAssay SIG
Bioconductor views DataRepresentation Infrastructure
Date of publicationNone
MaintainerMarcel Ramos <marcel.ramosperez@roswellpark.org>
LicenseArtistic-2.0
Version1.2.1
URL https://github.com/waldronlab/MultiAssayExperiment/wiki/MultiAssayExperiment-API
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("MultiAssayExperiment")

Man pages

API: Refer to the API documentation
assay-RangedRaggedAssay-missing-method: Create a Matrix of score values using a GRanges or own ranges
clusterOn: Check expression of a given feature against clinical variable
ExperimentList: Construct an 'ExperimentList' object for the...
ExperimentList-class: A container for multi-experiment data
hasAssay: Checking assay method for any class
mapToList: Convert map from data.frame or DataFrame to list and vice...
MultiAssayExperiment: Construct a 'MultiAssayExperiment' object
MultiAssayExperiment-class: An integrative multi-assay class for experiment data
MultiAssayExperiment-helpers: A group of helper functions for manipulating and cleaning a...
MultiAssayExperiment-methods: Accessing/modifying slot information
MultiAssayExperiment-package: MultiAssayExperiment: Build an integrative multi-assay...
prepMultiAssay: Prepare a 'MultiAssayExperiment' instance
RangedRaggedAssay: Create a RangedRaggedAssay
RangedRaggedAssay-class: An extension of the GRangesList class
subsetByAssay: Subset 'MultiAssayExperiment' object by Assay type
subsetByColData: Subset 'MultiAssayExperiment' object by 'colData' rows
subsetByColumn: Subset 'MultiAssayExperiment' object
subsetByRow: Subset 'MultiAssayExperiment' object by Feature
upsetSamples: Create a generalized Venn Diagram analog for sample...

Functions

$,MultiAssayExperiment-method Man page
$<-,MultiAssayExperiment-method Man page
API Man page Source code
DollarNames.MultiAssayExperiment Source code
ExperimentList Man page
ExperimentList,ANY-method Man page
ExperimentList,missing-method Man page
ExperimentList-class Man page
MultiAssayExperiment Man page Source code
MultiAssayExperiment-class Man page
MultiAssayExperiment-helpers Man page
MultiAssayExperiment-methods Man page
RangedBracketSubsetRRA Source code
RangedRaggedAssay Man page Source code
RangedRaggedAssay-class Man page
[,MultiAssayExperiment,ANY,ANY,ANY-method Man page
[,MultiAssayExperiment,ANY-method Man page
[,RangedRaggedAssay,ANY,ANY,ANY-method Man page
[,RangedRaggedAssay,ANY-method Man page
[,RangedRaggedAssay,GRanges,ANY,ANY-method Man page
[,RangedRaggedAssay,GRanges-method Man page
[[,MultiAssayExperiment,ANY,ANY-method Man page
[[<-,MultiAssayExperiment,ANY,ANY-method Man page
allIn Source code
apiDash Source code
assay,ANY,missing-method Man page
assay,ExperimentList,character-method Man page
assay,ExperimentList,missing-method Man page Man page
assay,ExperimentList,numeric-method Man page
assay,MultiAssayExperiment,character-method Man page
assay,MultiAssayExperiment,missing-method Man page
assay,MultiAssayExperiment,numeric-method Man page
assay,RangedRaggedAssay,missing-method Man page
assays,ExperimentList-method Man page
assays,MultiAssayExperiment-method Man page
c,MultiAssayExperiment-method Man page
checkExperimentList Source code
checkExperimentListNames Source code
checkGRL Source code
checkMethodsTable Source code
checkOverlapsAny Source code
checkSampleMapNames Source code
checkSampleNames Source code
cleanC Source code
cleanT Source code
clusterOn Man page Source code
colData,MultiAssayExperiment-method Man page
colData<-,MultiAssayExperiment,DataFrame-method Man page
complete.cases,MultiAssayExperiment-method Man page
dim,RangedRaggedAssay-method Man page
dimnames,ExperimentList-method Man page
dimnames,MultiAssayExperiment-method Man page
dimnames,RangedRaggedAssay-method Man page
dimnames<-,RangedRaggedAssay,list-method Man page
disjoin,RangedRaggedAssay-method Man page
duplicated Man page
duplicated,MultiAssayExperiment-method Man page
experiments Man page
experiments,MultiAssayExperiment-method Man page
experiments<- Man page
experiments<-,MultiAssayExperiment,ExperimentList-method Man page
findNumericMcol Source code
generateMap Source code
getColNamesErr Source code
getHits Source code
getMethErr Source code
getRowNamesErr Source code
harmonize Source code
hasAssay Man page Source code
hasOldAPI Source code
intersectColumns Man page Man page Source code
intersectRows Man page Source code
isEmpty,MultiAssayExperiment-method Man page
length,MultiAssayExperiment-method Man page
listToMap Man page Source code
longFormat Man page
longFormat,ANY-method Man page
longFormat,ExperimentList-method Man page
longFormat,MultiAssayExperiment-method Man page
longFormat,RangedRaggedAssay-method Man page
mapToList Man page Source code
matchReorderSub Source code
mergeReplicates Man page Man page
mergeReplicates,ANY-method Man page
mergeReplicates,ExperimentList-method Man page
mergeReplicates,MultiAssayExperiment-method Man page
mergeReplicates,RangedRaggedAssay-method Man page
metadata,MultiAssayExperiment-method Man page
metadata<-,MultiAssayExperiment-method Man page
names,MultiAssayExperiment-method Man page
pData,MultiAssayExperiment-method Man page
pData<-,MultiAssayExperiment,DataFrame-method Man page
packageAPI Source code
prepMultiAssay Man page Source code
rearrangeMap Source code
rowIdx Source code
sBracketSubsetRRA Source code
sEmpty Source code
sampleMap Man page
sampleMap,MultiAssayExperiment-method Man page
sampleMap<- Man page
sampleMap<-,MultiAssayExperiment,DataFrame-method Man page
show,ExperimentList-method Man page
show,MultiAssayExperiment-method Man page
show,RangedRaggedAssay-method Man page
splitArgs Source code
subsetByAssay Man page
subsetByAssay,MultiAssayExperiment-method Man page
subsetByColData Man page
subsetByColData,MultiAssayExperiment,ANY-method Man page
subsetByColData,MultiAssayExperiment,character-method Man page
subsetByColumn Man page
subsetByColumn,MultiAssayExperiment,List-method Man page
subsetByColumn,MultiAssayExperiment,list-method Man page
subsetByRow Man page
subsetByRow,MultiAssayExperiment,ANY-method Man page
subsetByRow,MultiAssayExperiment,List-method Man page
subsetByRow,MultiAssayExperiment,list-method Man page
subsetMultiAssayExperiment Source code
uniqueNamesInAssays Source code
uniqueSortIdentical Source code
updateObject,MultiAssayExperiment-method Man page
upsetSamples Man page Source code
validExperimentList Source code
validMultiAssayExperiment Source code
wideFormat Man page
wideFormat,ANY-method Man page
wideFormat,ExperimentList-method Man page
wideFormat,MultiAssayExperiment-method Man page

Files

DESCRIPTION
NAMESPACE
R
R/API.R
R/ExperimentList-class.R
R/MultiAssayExperiment-class.R
R/MultiAssayExperiment-helpers.R
R/MultiAssayExperiment-methods.R
R/MultiAssayExperiment-pkg.R
R/MultiAssayExperiment.R
R/RangedRaggedAssay-class.R
R/assay-methods.R
R/clusterOn.R
R/hasAssay.R
R/listToMap.R
R/mapToList.R
R/prepMultiAssay.R
R/upsetSamples.R
build
build/vignette.rds
inst
inst/NEWS
inst/doc
inst/doc/MultiAssayExperiment.R
inst/doc/MultiAssayExperiment.Rmd
inst/doc/MultiAssayExperiment.html
inst/doc/QuickStartMultiAssay.R
inst/doc/QuickStartMultiAssay.Rmd
inst/doc/QuickStartMultiAssay.html
inst/doc/UsingHDF5Array.R
inst/doc/UsingHDF5Array.Rmd
inst/doc/UsingHDF5Array.html
inst/doc/pradMAEO-RTCGAToolbox.R
inst/doc/pradMAEO-RTCGAToolbox.Rmd
inst/doc/pradMAEO-RTCGAToolbox.html
inst/extdata
inst/extdata/exMatrix.R
inst/extdata/exMatrix.h5
inst/extdata/hnscSample.rds
inst/extdata/hsncSample.R
inst/scripts
inst/scripts/ExperimentList-Ex.R
inst/scripts/MultiAssayExperiment-Ex.R
inst/scripts/MultiAssayExperiment-methods-Ex.R
inst/scripts/RangedRaggedAssay-Ex.R
inst/scripts/listToMap-Ex.R
man
man/API.Rd
man/ExperimentList-class.Rd
man/ExperimentList.Rd
man/MultiAssayExperiment-class.Rd
man/MultiAssayExperiment-helpers.Rd
man/MultiAssayExperiment-methods.Rd
man/MultiAssayExperiment-package.Rd
man/MultiAssayExperiment.Rd
man/RangedRaggedAssay-class.Rd
man/RangedRaggedAssay.Rd
man/assay-RangedRaggedAssay-missing-method.Rd
man/clusterOn.Rd
man/hasAssay.Rd
man/mapToList.Rd
man/prepMultiAssay.Rd
man/subsetByAssay.Rd
man/subsetByColData.Rd
man/subsetByColumn.Rd
man/subsetByRow.Rd
man/upsetSamples.Rd
tests
tests/testthat
tests/testthat.R
tests/testthat/test-ExperimentList-class.R
tests/testthat/test-Formats.R
tests/testthat/test-MultiAssayExperiment.R
tests/testthat/test-colnameOrder.R
tests/testthat/test-combine.R
tests/testthat/test-constructors.R
tests/testthat/test-drop.R
tests/testthat/test-emptybuilders.R
tests/testthat/test-map-manip.R
tests/testthat/test-mergeReps-colorder.R
tests/testthat/test-mergeReps.R
tests/testthat/test-methods.R
tests/testthat/test-rowcolnames.R
tests/testthat/test-subset.R
vignettes
vignettes/MultiAssayExperiment.Rmd
vignettes/QuickStartMultiAssay.Rmd
vignettes/UsingHDF5Array.Rmd
vignettes/extras
vignettes/extras/Fig1a.R
vignettes/extras/Fig1b.R
vignettes/extras/MAE-curatedMetagenomicData.Rmd
vignettes/pradMAEO-RTCGAToolbox.Rmd
MultiAssayExperiment documentation built on May 23, 2017, 10:01 a.m.