Changes in version 1.14                         

QFeatures 1.14.2

  - Fix bug in QFeatures::longFormat() when rownames are numerical
    (reported upstream
    https://github.com/waldronlab/MultiAssayExperiment/issues/331).

QFeatures 1.14.1

  - Import reshape2::melt, required for
    MultiAssayExperiment::longFormat().

QFeatures 1.14.0

  - New Bioc release 3.19

                        Changes in version 1.13                         

QFeatures 1.13.7

  - Fix filterFeatures() when the filter variable also exists in the
    global environment (issue #208).

QFeatures 1.13.6

  - Migrate .splitS[C]E() unit test form scp to QFeatures.

QFeatures 1.13.5

  - Reuse readQFeatres() params in readQFeatureFromDIANN().

QFeatures 1.13.4

  - Use DIA-NN example data from MsDataHub in readQFeaturesFromDIANN().

QFeatures 1.13.3

  - Fix is.vector() (see issue #203)
  - readQFeatures() multi-set support (ported from scp::readSCP() - see
    issue #199).
  - new readQFeaturesFromDIANN() function to import DIA-NN report files
    (ported from scp::readSCPfromDIANN() - see issue #199).

QFeatures 1.13.2

  - Move the filterFeatures generic method to ProtGenerics.

QFeatures 1.13.1

  - Fix typo in vigette.

                        Changes in version 1.11                         

QFeatures 1.11.2

  - Update message to fix test upon recent changes in MAE.

QFeatures 1.11.1

  - Update nNA() and filterNA() and man pages to clarify percentages and
    proportions (see #189).

QFeatures 1.11.0

  - New Bioconductor 3.18 (stable) release

                        Changes in version 1.10                         

QFeatures 1.10.0

  - New Bioconductor 3.17 (stable) release

                         Changes in version 1.9                         

QFeatures 1.9.4

  - New dropEmptyAssays() function (see issue #184).

QFeatures 1.9.3

  - Minor rephrasing in vignette and README.

QFeatures 1.9.2

  - feat: filterFeatures() now allows to select assays to filter (i
    argument)
  - feat: aggregateFeatures() can now take multiple assays
  - feat: impute() can now take multiple assays
  - feat: processing functions (normalize, scaleTransform, logTransform,
    sweep) can now take multiple assays
  - refactor: avoid validObject() when possible
  - Use |> rather than %>%.

QFeatures 1.9.1

  - fix: solved bug in selectRowData()

QFeatures 1.9.0

  - New Bioconductor 3.17 (devel) release

                         Changes in version 1.8                         

QFeatures 1.8.0

  - New Bioconductor 3.16 (stable) release

                         Changes in version 1.7                         

QFeatures 1.7.3

  - fix: fixed filterFeatures when selection contains environment
    variables

QFeatures 1.7.2

  - feat: added c methods to combine QFeatures objects.
  - feat: added nrows and ncols methods. Also added use.names argument
    (cf ?BiocGenerics::dims)
  - docs: improved docs for filterFeatures()
  - tests: improved unit tests for filterFeatures()
  - feat: added a keep argument in filterFeatures() to control whether
    to keep or remove features for assays that do not contain the filter
    variable. Also added message printing for a better overview of which
    variable were found.
  - fix: fixed addAssay() to solve issue #104.
  - refactor: refactored addAssay() and dramatically improved the usage
    of computational resources.
  - feat: colData is automatically transferred from the assay to the
    QFeatures object.
  - feat: implemented removeAssay() and replaceAssay(). Together with
    addAssay(), these functions are used to implement the replacement
    method [[<- required to solve issue #57.
  - Add CC-BY-SA license for vignettes.

QFeatures 1.7.1

  - refactor: imputation now adds a new assay instead of replacing
    values.

QFeatures 1.7.0

  - New Bioc devel version.

                         Changes in version 1.5                         

QFeatures 1.5.3

  - feat: aggregation by adjacency matrix
  - New adjacencyMatrix,SummarizedExperiment and
    adjacencyMatrix,QFeatures methods using
    ProtGenerics::adjacencyMatrix (available in version >= 1.27.1).

QFeatures 1.5.2

  - fix: implemented an updateObject() method for QFeatures objects.

QFeatures 1.5.1

  - Document the use of peptide/protein adjacency matrices in
    aggregateFeatures() and new adjacencyMatrix() accessor.

QFeatures 1.5.0

  - New devel version (Bioc 3.15)

                         Changes in version 1.3                         

QFeatures 1.3.6

  - New feat3 example data to demonstrate and test more complex
    AssayLinks structure.
  - Improved the plot,QFeautres function to avoid cluttering of nodes.
  - Adapted the visualization vignette using feat3.

QFeatures 1.3.5

  - Add plot,QFeatures and visualisation vignette.

QFeatures 1.3.4

  - Fixed bug that produced invalid AssayLinks when using filterNA.

QFeatures 1.3.3

  - Improved validity checks on AssayLinks
  - Fixed the subsetting of AssayLinks to ensure consistent data

QFeatures 1.3.2

  - Add logo to package
  - Fix class coercion error (see #b9ce7f1e9)

QFeatures 1.3.1

  - Added rbindRowData: a function to select variables in the rowData
    and bind it in a single DataFrame
  - Added rowData<-: this new method replaces replaceRowDataCols to
    offer a more standardize functionality.
  - Added a new section in the QFeatures vignette to expand on how to
    manipulate the metadata within a QFeatures object

QFeatures 1.3.0

  - New devel version (Bioc 3.14)

                        Changes in version 1.2.0                        

QFeatures 1.2.0

  - New release version (Bioc 3.13)

                        Changes in version 1.1.0                        

QFeatures 1.1.4

  - Added replaceRowDataCols and removeRowDataCols, two functions to
    streamline manipulation of rowData within a QFeature object.

QFeatures 1.1.3

  - Added countUniqueFeatures, a function to count the number of unique
    features per sample.

QFeatures 1.1.2

  - Manually install preprocessCore (see
    https://github.com/Bioconductor/bioconductor_docker/issues/22 for
    details) to use quantile normalisation in vignette and tests.

  - Update vignette to show normalize() and logTransform() directly on a
    QFeatures object and reference the QFeaturesWorkshop2020 workshop
    and WSBIM2122 chap 8.

QFeatures 1.1.1

  - Fix typo in vignette
  - Improve first paragraph in intro vignette.

QFeatures 1.1.0

  - New Bioconductor devel version

                        Changes in version 0.99                         

QFeatures 0.99.4

  - Fix: improved nNA with new implementation and additional unit tests
    <2020-10-23 Fri>

QFeatures 0.99.3

  - New feature: the longFormat function returns a long DataFrame with
    quantitative data along with metadata (see #116) <2020-10-8 Thu>
  - New feature: the rowData method returns a list containing the
    rowData for all assays (see #86) <2020-09-16 Wed>
  - Keep colnames when reading a single column assay (see #108)
    <2020-09-09 Wed>

QFeatures 0.99.2

  - Added infIsNA.
  - Add Christophe Vanderaa as an author.

QFeatures 0.99.1

  - Address comments Bioconductor review (see submission issue for
    details.

QFeatures 0.99.0

  - Bioconductor submission