Changes in version 2.24.0                        

Bug fixes and minor improvements

  - The deprecated functionality vignette moved to the
    vignettes/analysis/ folder

                       Changes in version 2.22.0                        

New features

  - makeSummarizedExperimentFromGISTIC transferred from TCGAutils

Bug fixes and minor improvements

  - biocExtract now merges datasets from the same platforms
  - Re-worked and simplified getData method for FirehoseData and
    FirehoseGISTIC
  - Remove missing ranges when creating GRanges and GRangesList from
    DataFrame

                       Changes in version 2.20.0                        

New features

  - Added the RNASeq2Gene slot to the FirehoseData class. This data type
    mainly obtains RNASeq v2 raw_counts from the pipeline
    (scaled_estimates also available; @mherberg #39)
  - Added an accmini example dataset as obtained from getFirehoseData
  - getLinks function shows the user some file provenance based on data
    requested
  - Newly deprecated functions: getDiffExpressedGenes,
    getCNGECorrelation, getSurvival and getReport. It is no longer
    possible for the maintainer to update these functions in a way that
    would benefit users. A transfer of responsibility would be required,
    i.e. to another package.
  - Vignettes are updated to reflect changes in the codebase.

Bug fixes and minor improvements

  - Improvements to internal functions for converting tabular data to
    Bioconductor classes
  - Missing (NA) seqnames are removed when converting to
    RaggedExperiment
  - Remove static file dependencies from GitHub and use text inside
    function (@DavisWeaver, #34)
  - Added default values to helper for making SummarizedExperiment
    datasets
  - Coerce sample names to character when in (the rare) case they're
    numeric
  - Added an ellipsis argument to biocExtract for specifying the
    names.field in tabular data that will correspond to the row names of
    a SummarizedExperiment

                       Changes in version 2.18.0                        

New features

  - Warning for Windows users added when file paths are too long
  - getGISTICPeaks now requires a FirehoseGISTIC data object obtained
    from getFirehoseData

Bug fixes and minor improvements

  - Consolidate GISTIC data download methods in getFirehoseData and
    getGISTICPeaks
  - Increase robustness of internal helper functions that work with
    strands
  - 'TCGA' sample column identification is less strict

                       Changes in version 2.16.0                        

New features

  - RNASeq2GeneNorm slot in the FirehoseData class is a list now (from
    matrix)
  - Use tempdir() as the default directory for downloading data in
    getFirehoseData

Bug fixes and minor improvements

  - Save all RNASeq2GeneNorm datasets within the output object as a
    list. Previously, only the last dataset would get returned (#30)
  - Read files from the appropriate download location in getFirehoseData
  - Move static text file references from 'canevolve.org' to GitHub
    hosted locations
  - Check file sizes using httr instead of 'canevolve.org' query
    (@mksamur, #32)

                       Changes in version 2.14.0                        

Bug fixes and minor improvements

  - GISTIC data for SKCM and LAML is correctly returned by the
    getFirehoseData function
  - Helpers now correctly assign row names in presence of ranged data
    when using biocExtract

                       Changes in version 2.12.0                        

New features

  - biocExtract can now return GISTIC peak data as well with the
    'GISTICP' option
  - Methylation data is now converted to DelayedArray and contained in
    SummarizedExperiment objects via biocExtract
  - Added an isEmpty method to the FirehoseGISTIC data class

Bug fixes and minor improvements

  - Set default 'peak' argument to 'wide'
  - Functionality from the TCGAutils package is now employed such as
    findGRangesCols and uniformBuilds

                       Changes in version 2.9.41                        

Bug fixes and minor improvements

  - Fixed bug where file rename was not working due to incorrect path
    location in getFirehoseData

                       Changes in version 2.9.40                        

New features

  - getBroadSubtypes and getGISTICPeaks now included in the package.
    Thanks to @lgeistlinger!
  - Updated import directives
  - Added peaks data slot to the FirehoseGISTIC class
  - Numerous improvements to internal helpers
  - Added a GISTIC argument to getFirehoseData

                       Changes in version 2.7.44                        

New features

  - selectType function replaces all previous data type extractor
    functions
  - getData improved, removed CN argument
  - Cleaner documentation for biocExtract

Bug fixes and minor improvements

  - Included helper functions for enabling full functionality of
    biocExtract
  - Added appropriate import directives
  - Re-organized documentation for readability

                       Changes in version 2.7.21                        

New features

  - biocExtract function now available - convert data objects to
    Bioconductor friendly data classes

New features

  - New maintainer for package
  - Updated API - see FirehoseData slots for changes
  - New extractor functions for slots of FirehoseData
  - Standardize argument names and slots
  - Export functions in package
  - Updated NAMESPACE

Bug fixes and minor improvements

  - Cleaner documentation
  - Import directives appropriate
  - Example dataset updated to new API