NEWS.md

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

MultiAssayExperiment 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)

MultiAssayExperiment 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)

MultiAssayExperiment 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

MultiAssayExperiment 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

MultiAssayExperiment 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

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

MultiAssayExperiment 1.7.14

New features

• 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

• 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, #)

MultiAssayExperiment 1.5.108

New features

• DataFrame now exported for users (@DarioS, #242)
• c is smarter at matching colnames with primary names and creating a sampleMap

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

MultiAssayExperiment 1.5.102

New features

• The MatchedAssayExperiment constructor function now works either a single MultiAssayExperiment or the essential components of one.

MultiAssayExperiment 1.5.101

New features

• Renamed duplicated function to replicated
• Added coercion functions from List and list to ExperimentList
• Improve speed of reshape functions from previous change (wideFormat)

Bug fixes and minor improvements

• 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

MultiAssayExperiment 1.5.65

Bug fixes and minor improvements

• 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)

MultiAssayExperiment 1.5.64

New features

• Remove clusterOn function and move to Bioconductor/MultiOmicQC package on GitHub

MultiAssayExperiment 1.5.63

New features

• duplicated has been deprecated, use replicated and anyReplicated
• removed dependencies on tidyr and reshape2

Bug fixes and minor improvements

• Updates to prepMultiAssay
• Enhancements to the main vignette
• New format for NEWS section

MultiAssayExperiment 1.5.38

New features

• 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

• 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)
• Improved test scripts

MultiAssayExperiment 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

MultiAssayExperiment 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

MultiAssayExperiment 1.1.52

New features

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

MultiAssayExperiment 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

MultiAssayExperiment 1.1.44

Bug fixes and minor improvements

• Renamed PrepMultiAssay to prepMultiAssay (lower p following convention)

MultiAssayExperiment 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

MultiAssayExperiment 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

MultiAssayExperiment 1.1.17

New features

• upsetSamples function implemented

MultiAssayExperiment 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

MultiAssayExperiment 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

MultiAssayExperiment 1.1.12

New features

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

MultiAssayExperiment 1.1.11

New features

• Renamed gather function to collect

MultiAssayExperiment 1.1.10

New features

• Double bracket method for MultiAssayExperiment available

MultiAssayExperiment 1.1.9

New features

• clusterSex function available for clustering gender from expression data

Bug fixes and minor improvements

• Improvements to documentation

MultiAssayExperiment 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

MultiAssayExperiment 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

MultiAssayExperiment 1.1.1

New features

• MultiAssayExperiment now in release!
• extract method not available for common classes - creates tidy data.frame from data

Bug fixes and minor improvements

• Documentation updated with new roxygen version

MultiAssayExperiment 0.101.49

New features

• Example section added to vignette for converting data frames to Bioconductor objects

Minor improvements

• A proper dimnames method added to MultiAssayExperiment

MultiAssayExperiment 0.101.45

New features

• dimnames method added to RangedRaggedAssay

Bug fixes and minor improvements

• Improved RangedRaggedAssay rowname construction
• Improved show method for the RangedRaggedAssay class

MultiAssayExperiment 0.101.44

New features

• $ (DollarSign) method available for MultiAssayExperiment to access pData column

MultiAssayExperiment 0.101.43

Bug fixes and minor improvements

• Improved MultiAssayExperiment constructor now handles stray assays, colnames, pData rownames, and sampleMap rows

MultiAssayExperiment 0.101.42

New features

• metadata<- set method now available for the MultiAssayExperiment

Bug fixes and minor improvements

• metadata argument available in the MultiAssayExperiment constructor function
• Fix bug when subsetting for unmatched samples/colnames (drop = FALSE) in constructor

MultiAssayExperiment 0.101.40

New features

• Improved MultiAssayExperiment constructor with renamed argument "experiments" for the ExperimentList or list input.

MultiAssayExperiment 0.101.39

New features

• updateObject method now available for old instances of the MultiAssayExperiment
• Users with invalid MultiAssayExperiments should update and re-serialize them

Bug fixes and minor improvements

• drop argument now works as intended when using List inherited objects

MultiAssayExperiment 0.101.38

New features

• complete.cases method available for the MultiAssayExperiment class

MultiAssayExperiment 0.101.37

New features

• sampleMap column names renamed to assay (prev. "assayname"), primary, and colname (prev. "assay")
• New vignete available for creating MultiAssayExperiment objects with TCGA data

Bug fixes and minor improvements

• Added informative error to MultiAssayExperiment constructor
• Improved show method display
• Removed warning message when only ExperimentList argument provided

MultiAssayExperiment 0.101.36

• 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

MultiAssayExperiment 0.101.34

• assay method for RangedRaggedAssay works on inner metadata columns now
• vignette examples available for HDF5Array package
• Improved outline for main vignette

MultiAssayExperiment 0.99.202

New features

• assay method available for RangedRaggedAssay and other classes. Created to obtain raw data from certain classes (see ?assay,(class),ANY-method).

MultiAssayExperiment 0.99.194

New features

• 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

Bug fixes and minor improvements

• superflous subset function removed
• sampleMap uses character vectors instead of Rle
• Elist order consistent when subsetting
• mapToList preserves list order

MultiAssayExperiment 0.99.14

• NEWS file is now live!
• Package now in Bioc-devel!
• More to come!

New features

• Replacement method for colnames now available for the RangedRaggedAssay class.

Bug fixes and minor improvements

• Documentation additions

MultiAssayExperiment documentation built on Nov. 8, 2020, 8:10 p.m.