Changes in version 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 Changes in version 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 Changes in version 101.44 New features - $ (DollarSign) method available for MultiAssayExperiment to access pData column Changes in version 101.43 Bug fixes and minor improvements - Improved MultiAssayExperiment constructor now handles stray assays, colnames, pData rownames, and sampleMap rows Changes in version 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 Changes in version 101.40 New features - Improved MultiAssayExperiment constructor with renamed argument "experiments" for the ExperimentList or list input. Changes in version 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 Changes in version 101.38 New features - complete.cases method available for the MultiAssayExperiment class Changes in version 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 Changes in version 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 Changes in version 101.34 - assay method for RangedRaggedAssay works on inner metadata columns now - vignette examples available for HDF5Array package - Improved outline for main vignette Changes in version 9.202 New features - assay method available for RangedRaggedAssay and other classes. Created to obtain raw data from certain classes (see ?assay,(class),ANY-method). Changes in version 9.194 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 Changes in version 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 Changes in version 5.102 New features - The MatchedAssayExperiment constructor function now works either a single MultiAssayExperiment or the essential components of one. Changes in version 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 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 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 Changes in version 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, #) Changes in version 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) Changes in version 1.5.64 New features - Remove clusterOn function and move to Bioconductor/MultiOmicQC package on GitHub Changes in version 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 Changes in version 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 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 - 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 Changes in version 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