NEWS.md

Changes in version 1.32.0

Bug fixes and minor improvements

• Various documentation improvements to MultiAssayExperimenToMAF, saveHDF5MultiAssayExperiment, and reexports
• When rownames are numeric characters e.g., "1", ensure they stay character when converting MultiAssayExperiment to longFormat.

Changes in version 1.30.2

Bug fixes and minor improvements

• The colData<- replacement method now correctly works with data.frame value inputs (@drighelli, #330).
• Updated CITATION information in the main vignette.
• Use reshape2::melt instead of stats::reshape to preserve row names in longFormat

Changes in version 1.28.0

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.

Changes in version 1.26.0

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

Changes in version 1.24.0

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)

Changes in version 1.22.0

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

Changes in version 1.20.0

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.

Changes in version 1.18.0

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

Changes in version 1.16.0

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)

Changes in version 1.14.0

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)

Changes in version 1.12.0

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

Changes in version 1.10.0

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

Changes in version 1.8.0

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, #)

Changes in version 1.6.0

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)

Changes in version 1.1.59

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

Changes in version 1.1.52

New features

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

Changes in version 1.1.49

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

Changes in version 1.1.44

Bug fixes and minor improvements

• Renamed PrepMultiAssay to prepMultiAssay (lower p following convention)

Changes in version 1.1.43

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

Changes in version 1.1.37

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

Changes in version 1.1.27

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

Changes in version 1.1.17

New features

• upsetSamples function implemented

Changes in version 1.1.16

New features

• Implement shape argument for rearrange function: wide now available

Bug fixes and minor improvements

• Updated vignettes: DelayedMatrix & PRAD MultiAssayExperiment object

Changes in version 1.1.15

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

Changes in version 1.1.12

New features

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

Changes in version 1.1.11

New features

• Renamed gather function to collect

Changes in version 1.1.10

New features

• Double bracket method for MultiAssayExperiment available

Changes in version 1.1.9

New features

• clusterSex function available for clustering gender from expression data

Bug fixes and minor improvements

• Improvements to documentation

Changes in version 1.1.6

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

Changes in version 1.1.2

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

Changes in version 1.1.1

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