New features

  • Dropped experiments are no longer kept in the metadata slot. They can be seen with drops() (@LTLA, #323).

Bug fixes and minor improvements

  • Checking colnames in sampleMap vs ExperimentList is more robust by only comparing unique and sorted values in each.

New features

  • showReplicated displays the actual colnames of technical replicates by assay and biological unit.
  • The bracket replacement method [<- for MultiAssayExperiment now also replaces the names with those from the right-hand side of the operation, if any (@DarioS, #319)

Bug fixes and minor improvements

  • During single assay replacement [[<-, the re-ordering of assays based on the value input was invalid when empty assays present (@danielinteractive, #322).
  • Permuting assays also updates the order of names in the MultiAssayExperiment and assays in the sampleMap

New features

  • replicates provides the actual colnames identified as replicate observations for a particular biological unit in the sampleMap

Bug fixes and minor improvements

  • Added an assay<- replacement method for robustifying saveHDF5MultiAssayExperiment with plain matrices
  • Use BiocBaseUtils::setSlots and avoid warnings of triple colon use.
  • Resolve issue when colData has one column when merging two MultiAssayExperiment objects, i.e., using the c method (@cvanderaa, #315)
  • Increase efficiency in colnames and rownames methods (@cvanderaa, #314)
  • Make ‘prefix’ inputs consistent in saveHDF5MultiAssayExperiment and loadHDF5MultiAssayExperiment (@asiyeka, #313)
  • Improve performance for replicated method
  • Update wideFormat documentation, when replicates present additional sets of columns will be appended to the produced DataFrame (@DarioS, #312)

Bug fixes and minor improvements

  • Add data("miniACC") to examples after removing lazy loading.
  • Class definition prototypes defined for cleaner extensibility (@hpages, #306).
  • Doc and internal improvments to MultiAssayExperimentToMAF
  • synAssay and nonSynAssay now require exact assay names in MultiAssayExperimentToMAF

Bug fixes and minor improvements

  • Avoid dropping experiments with repeated calls to subsetByColData and remove harmonization (@cvanderaa, #302)
  • getWithColData suppresses messages from natural subsetting operations by default with verbose = FALSE (@bhagwataditya, #301)
  • getWithColData was using the old default (drop = TRUE) and causing an error when the experiment is empty (@danielinteractive, #300).
  • Calls to the internal .harmonize operation are reduced to increase memory efficiency, when identical experiment colnames present (@LTLA, #299).
  • subsetByColData now errors on subscript vectors longer than the nrow of the colData (previously a warning).
  • colData<- includes a check for identical row names. If so, direct replacement of the colData occurs without harmonization.
  • Added a warning when an empty sampleMap is provided in the constructor function which may cause unexpected behavior. Documentation is updated to include more details on the sampleMap input.

New features

  • saveHDF5MultiAssayExperiment allows users to save data from most classes (excluding RaggedExperiment) into a single H5 file (ctb @hpages)
  • Support for maftools conversion has been added as MultiAssayExperimentToMAF (ctb @PoisonAlien)
  • renameColname and renamePrimary provide renaming facilities for column names in experiments and rownames in the colData, respectively
  • Users can now rename some or all the column names in experiments using colnames(mae) <- value
  • When replacing colData or experiments (including [[<-), new rownames and colnames (respectively) are checked against existing values and an error is given when none match
  • Using List objects to replace the data in the ExperimentList is now supported
  • splitAssay allows users to separate / split columns across assays
  • makeHitList is a facilitator function to create the logical lists that are required as input to splitAssay
  • drop argument when subsetting a MultiAssayExperiment is now FALSE by default

Bug fixes and minor improvements

  • Updated the constructor function to auto-populate rownames in colData when it is missing (@LTLA, #287)
  • The metadata now includes names of dropped experiments
  • Updated validity checks to support array-like classes
  • Dropped experiments are tracked in the metadata

New features

  • Coercion methods from list/List to MultiAssayExperiment method now available.

Bug fixes and minor improvements

  • Provide more details in documentation for mergeReplicates
  • Improved documentation for accessor function return values, helper function examples (@llrs, #281)
  • Fixed bug when using longFormat with character assay matrices (@jonocarroll, #282)

New features

  • exportClass creates a number of .csv data files for exporting data
  • Allow vector input i for selecting assays in longFormat (@lgatto, #266)
  • Updates to ‘Using MultiAssayExperiment with DelayedMatrix’ vignette

Bug fixes and minor improvements

  • Warn when colData rownames and ExperimentList colnames are empty (@LTLA #262)
  • Add informative error message for ExperimentList (@lgatto, #265)
  • Informative warning when dropping ExperimentList element columns (@lwaldron)
  • Fixes to constructor functions, MultiAssayExperiment and MatchedAssayExperiment (@lgatto, #267 #268, @lwaldron)
  • Add warning when j in mae[i, j, k] is longer than colData rows
  • Strict argument matching between generic and methods
  • Updates due to class(matrix())
  • UpsetSamples more robust to differences in names between split sampleMap and names(ExperimentList) (@jonocarroll, #269)
  • Refactored and improved UpsetSamples
  • ExperimentList propagation of mcols and metadata (@vobencha, #270)
  • Enforcement of validObject with replacement methods colData and sampleMap (@vobencha, #271)

Bug fixes and minor improvements

  • Improvements to the main vignette, MultiAssayExperiment class schematic now included (@mtmorgan, #261)
  • Updated documentation for the upsetSamples function
  • Update code to use splitAsList from S4Vectors (@hpages)
  • Fixed bug with metadata disappearing from ExperimentList when replacing it inside a MultiAssayExperiment object (@lawremi, #259)
  • Fixed the formatting of the NEWS file

New features

  • getWithColData now allows easy extraction of experiments (such as SummarizedExperiment) with associated colData data
  • Single bracket replace method implemented for MultiAssayExperiment assays

Bug fixes and minor improvements

  • isEmpty method fixed for ExperimentLists containing matrices
  • MultiAssayExperiment now inherits from the standard Annotated virtual class
  • c method better distinguishes between list and ExperimentList inputs
  • Improvements on .getHits internal method for obtaining correct queries on row metadata
  • Subsetting mechanism tweaked to do nothing when subsetting by NULL rows compared to empty rows (i.e., character(0L))
  • Improved README.md

New features

  • The single bracket replacement method [<- added to support assignment of assay datasets
  • Users can now rename experiments in a MultiAssayExperiment with names(x) <- value
  • replicated and mergeReplicates functions have been refactored and improved
  • combining MultiAssayExperiments now possible with c function
  • Subsetting MultiAssayExperiment by a list or List type class now returns experiments in the input order for rows, columns, and assays

Bug fixes and minor improvements

  • wideFormat function improvements and bug fixes with name indicator subsetting
  • BiocGenerics:::replaceSlots used instead of replace methods
  • Added tests for anyReplicated, c, and names<- functions
  • Unit tests added for replacement method testing
  • Renamed objects in examples for brevity and descriptiveness
  • Updated importFrom directives
  • Internal sample names check now only works on non-empty colnames
  • Various documentation improvements
  • listToMap re-written for efficiency
  • Various improvements to subsetting mechanism
  • subsetByAssay bug fixed when using an integer index (@vjcitn, #)

New features

  • DataFrame now exported for users (@DarioS, #242)
  • c is smarter at matching colnames with primary names and creating a sampleMap
  • The MatchedAssayExperiment constructor function now works either a single MultiAssayExperiment or the essential components of one.
  • Renamed duplicated function to replicated
  • Added coercion functions from List and list to ExperimentList
  • Improve speed of reshape functions from previous change (wideFormat)
  • Remove clusterOn function and move to Bioconductor/MultiOmicQC package on GitHub
  • duplicated has been deprecated, use replicated and anyReplicated
  • removed dependencies on tidyr and reshape2
  • Moved the API shiny function to waldronlab/MultiAssayShiny package
  • Reduced imports (removed shinydashboard and shiny)
  • Method requirement checks for classes are practical using try()
  • Deprecated methods removed: pData
  • Deprecated class removed: RangedRaggedAssay
  • Assay-selective subsetting implemented via list/List class subsettors

Bug fixes and minor improvements

  • Added an isEmpty method for ExperimentList to account for an empty matrix
  • Documentation improvements to MultiAssayExperiment-class and MultiAssayExperiment-helpers
  • c internals improved
  • Explicitly check for DataFrame in ExperimentList
  • Fixed documentation warnings for inexact links
  • Fix subsetting order in bracket method ([)
  • Minor vignette changes
  • Supply a collapse character for wideFormat column names
  • upsetSamples does not munge experiment names with special characters when check.names = FALSE (by default keeps hyphens, underscores, etc.). A nameFilter functional argument allows operations such as substr on the experiment names. (@vjcitn, #231)
  • Updates to prepMultiAssay
  • Enhancements to the main vignette
  • New format for NEWS section
  • updated duplicated function now returns FALSE for non-duplicated samples
  • Improved ExperimentList constructor now handles multiple key = value entries
  • Removed updateObject before giving warning
  • Removed old RTCGAToolbox example vignette
  • Official manuscript citation added
  • Improved examples (removed ExpressionSet legacy objects)

New features

  • rearrange is now broken up into longFormat and wideFormat functions.
  • Helper functions now have a dedicated man page, see: ?'MultiAssayExperiment-helpers'

Bug fixes and minor improvements

  • A subset can affect the order of rows (previously it didn’t)
  • rownames are exclusively used to create longFormat DataFrames
  • The longFormat,ExperimentList-method now returns a long DataFrame
  • Minor improvements to tests

New features

  • reduce removed and broken up into mergeReplicates and intersectColumns
  • Additional helper introduced: intersectRows

New features

  • pData deprecated in favor of colData
  • Quick start vignette now available

Bug fixes and minor improvements

  • Fixed API function link
  • Removed coercion to old RangedRaggedAssay class
  • Improved listToMap

Bug fixes and minor improvements

  • Renamed PrepMultiAssay to prepMultiAssay (lower p following convention)

New features

  • The MultiAssayExperiment quickstart guide vignette added
  • Deprecation of the RangedRaggedAssay class. Use RaggedExperiment package instead.
  • reduce function simplified
  • mapFrom convenience argument added to the c,MultiAssayExperiment-method
  • assay and assays methods have been revised to conform to SummarizedExperiment standards

Bug fixes and minor improvements

  • API() now points to the correct web document
  • ExperimentList constructor no longer coerces GRangesList to RangedRaggedAssay
  • Documentation changes: consolidate man pages for experiments, experiments<-, sampleMap, and sampleMap<-
  • removal of internal getHits method, simplified helper function in place
  • prepMultiAssay helper now returns a list with names corresponding to the MultiAssayExperiment constructor function

New features

  • MatchedAssayExperiment subclass added for matched samples in all assays
  • Supply mini ACC dataset data(miniACC)
  • Provide reference table for methods in package, see vignettes
  • Merge with GitHub development version

Bug fixes and minor improvements

  • ensure assay column in sampleMap is a factor
  • rearrange long DataFrame correctly
  • remove support for RangedRaggedAssay - deprecate
  • drop = FALSE in single column subset of colData
  • default sampleMap representation as empty DataFrame with colnames
  • added combine c vignette section for adding experiments to an existing

New features

  • c method implemented for experiments with 1:1 sample matches in pData rows
  • MultiAssayExperiment show method improved
  • Double bracket [[ extracts single experiment (replacement also included)
  • Internal getHits methods removed and refactored subsetByRows
  • subsetBypData available
  • rearrange method now supports “wide” format outputs

Bug fixes and minor improvements

  • Updates to HDF5 vignette
  • More examples to documentation
  • Numerous bug fixes
  • mapToList uses the more efficient splitAsList function

New features

  • upsetSamples function implemented

New features

  • Implement shape argument for rearrange function: wide now available

Bug fixes and minor improvements

  • Updated vignettes: DelayedMatrix & PRAD MultiAssayExperiment object

New features

  • disjoin method for RangedRaggedAssay

Bug fixes and minor improvements

  • show method for RangedRaggedAssay abbreviated. No longer summarizes data with assay
  • Documentation changes for reduce and disjoin

New features

  • gather/collect function name changed to rearrange
  • clusterSex now clusterOn, works with characteristic of choice

New features

  • Renamed gather function to collect

New features

  • Double bracket method for MultiAssayExperiment available

New features

  • clusterSex function available for clustering gender from expression data

Bug fixes and minor improvements

  • Improvements to documentation

New features

  • Added an example HNSC dataset

Bug fixes and minor improvements

  • Improve documentation of assay method for the RangedRaggedAssay
  • Bug fixes for assay method
  • Removed method pollution for other Bioconductor classes
  • assay method only shows numeric or character data

New features

  • extract method renamed to gather
  • gather allows for inclusion of pData columns
  • gather method supports common classes; creates a “tidy” DataFrame with pData rownames, ExperimentList rownames, ExperimentList columns, assay names, and optional pData columns

Bug fixes and minor improvements

  • Fix assay arguments for the RangedRaggedAssay method
  • Subsetting by column now arranges sampleMap in proper order

New features

  • extract method now available for common classes - creates tidy data.frame from data
  • Example section added to vignette for converting data frames to Bioconductor objects
  • dimnames method added to RangedRaggedAssay
  • $ (DollarSign) method available for MultiAssayExperiment to access pData column
  • metadata<- set method now available for the MultiAssayExperiment
  • Improved MultiAssayExperiment constructor with renamed argument “experiments” for the ExperimentList or list input.
  • updateObject method now available for old instances of the MultiAssayExperiment
  • Users with invalid MultiAssayExperiments should update and re-serialize them
  • complete.cases method available for the MultiAssayExperiment class
  • sampleMap column names renamed to assay (prev. “assayname”), primary, and colname (prev. “assay”)
  • New vignete available for creating MultiAssayExperiment objects with TCGA data
  • Elist class renamed to ExperimentList
  • ExperimentList constructor is homonymous
  • ExperimentList accessor now called experiments
  • ExperimentList replacement method is now experiments<-
  • Updated vignettes to reflect change of names
  • assay method for RangedRaggedAssay works on inner metadata columns now
  • vignette examples available for HDF5Array package
  • Improved outline for main vignette
  • assay method available for RangedRaggedAssay and other classes. Created to obtain raw data from certain classes (see ?assay,(class),ANY-method).
  • Subsetting by non-character i (#108)
  • PrepMultiAssay helper function now available to aid in creating object (#122)
  • Vignette now building (#125)
  • Preliminary assay method for RangedRaggedAssay
  • Replacement method for colnames now available for the RangedRaggedAssay class.

Bug fixes and minor improvements

  • Documentation updated with new roxygen version
  • Improved RangedRaggedAssay rowname construction
  • Improved show method for the RangedRaggedAssay class
  • Improved MultiAssayExperiment constructor now handles stray assays, colnames, pData rownames, and sampleMap rows
  • metadata argument available in the MultiAssayExperiment constructor function
  • Fix bug when subsetting for unmatched samples/colnames (drop = FALSE) in constructor
  • drop argument now works as intended when using List inherited objects
  • A proper dimnames method added to MultiAssayExperiment
  • Added informative error to MultiAssayExperiment constructor
  • Improved show method display
  • Removed warning message when only ExperimentList argument provided
  • Superfluous subset function removed
  • sampleMap uses character vectors instead of Rle
  • Elist order consistent when subsetting
  • mapToList preserves list order