# MultiAssayExperiment ---------------------------------------------------------------- ## 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 `ExperimentList`s 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 1.5.108 ### 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 1.5.102 ### New features * The `MatchedAssayExperiment` constructor function now works either a single `MultiAssayExperiment` or the essential components of one. ## Changes in version 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 ## 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 1.1.37 ### 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 1.1.59 ### 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` `DataFrame`s * 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 1.1.27 ### 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 0.101.49 ### 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 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 ## Changes in version 0.101.44 ### New features * `$` (DollarSign) method available for `MultiAssayExperiment` to access `pData` column ## Changes in version 0.101.43 ## Bug fixes and minor improvements * Improved `MultiAssayExperiment` constructor now handles stray assays, colnames, pData rownames, and `sampleMap` rows ## Changes in version 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 ## Changes in version 0.101.40 ### New features * Improved `MultiAssayExperiment` constructor with renamed argument "experiments" for the `ExperimentList` or `list` input. ## Changes in version 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 ## Changes in version 0.101.38 ### New features * `complete.cases` method available for the `MultiAssayExperiment` class ## Changes in version 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 ## Changes in version 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 ## Changes in version 0.101.34 * `assay` method for `RangedRaggedAssay` works on inner metadata columns now * vignette examples available for `HDF5Array` package * Improved outline for main vignette ## Changes in version 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`). ## Changes in version 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 ## 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