# 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 * `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 # MultiAssayExperiment 1.1.52 * `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