NEWS

MultiAssayExperiment 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.

MultiAssayExperiment 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

MultiAssayExperiment 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.

MultiAssayExperiment 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

MultiAssayExperiment 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)

MultiAssayExperiment 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

MultiAssayExperiment 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.

MultiAssayExperiment 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

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
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, #)

MultiAssayExperiment 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)

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 1.1.37

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 1.1.27

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

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