Changes in version 1.17                         

QFeatures 1.17.2

  - Fix fnames argument in readQFeatures(). The fnames argument is not
    passed to readSummarizedExperiment() anymore, but used at in
    readQFeatures(). Rownames are now set after splitting. Given that
    rownames must be unique and that this was enforced with
    make.unique(), the previous behaviour misnamed features that should
    get the same name.

QFeatures 1.17.1

  - Fix: solved readQFeatures() bug and adapted unit tests.
  - Docs: created new vignette about reading data with QFeatures

QFeatures 1.17.0

  - New Bioconductor 3.21 (devel) release

                        Changes in version 1.16                         

QFeatures 1.16.0

  - New Bioconductor 3.20 (stable) release

                        Changes in version 1.15                         

QFeatures 1.15.3

  - Fix typo in normalisation methods.

QFeatures 1.15.2

  - Fix bug in QFeatures::longFormat() when rownames are numerical
    (reported upstream
    https://github.com/waldronlab/MultiAssayExperiment/issues/331).
  - Starting New API unit test (see issue #214.

QFeatures 1.15.1

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

QFeatures 1.15.0

  - New Bioc devel

                        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