NEWS.md
In vjcitn/MultiAssayExperiment: Software for the integration of multi-omics experiments in Bioconductor

MultiAssayExperiment

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

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

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

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

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

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

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

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

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

pData deprecated in favor of colData
Quick start vignette now available

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

Renamed PrepMultiAssay to prepMultiAssay (lower p following convention)

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

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

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

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

upsetSamples function implemented

Implement shape argument for rearrange function: wide now available

Updated vignettes: DelayedMatrix & PRAD MultiAssayExperiment object

disjoin method for RangedRaggedAssay

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

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

Renamed gather function to collect

Double bracket method for MultiAssayExperiment available

clusterSex function available for clustering gender from expression data

Improvements to documentation

Added an example HNSC dataset

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

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

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

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

Documentation updated with new roxygen version

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

A proper dimnames method added to MultiAssayExperiment

dimnames method added to RangedRaggedAssay

Improved RangedRaggedAssay rowname construction
Improved show method for the RangedRaggedAssay class

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

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

metadata<- set method now available for the MultiAssayExperiment

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

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

drop argument now works as intended when using List inherited objects

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

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

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

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

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

Replacement method for colnames now available for the RangedRaggedAssay class.

Documentation additions

vjcitn/MultiAssayExperiment documentation built on May 3, 2019, 6:13 p.m.

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