Changelog

Source: NEWS.md

QFeatures 1.19

QFeatures 1.19.2

• Aggregate features optimisation.

QFeatures 1.19.1

• Fix duplicated fnames bug (see issue #237).
• Use longForm() methods (replacing longFormat(), now defunct).
• Add longForm,SummarizedExperiment, supporting rowvars and colvars, as longForm,QFeatures does. Without this method, uses longForm,ANY that doesn’t.
• Defined a QFeatures object type (bulk or single-cell) in the instance’s metadata slot (developer features).

QFeatures 1.19.0

• New devel version

QFeatures 1.17

QFeatures 1.17.5

• Remove superfluous message when filtering with keep = TRUE (see issue 231).

QFeatures 1.17.4

• Optimisation of aggregateFeatures in the case of multiple assays aggregation.

QFeatures 1.17.3

• Fix bug in nNA() on empty assays (see #174).

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

QFeatures 1.16

QFeatures 1.16.0

• New Bioconductor 3.20 (stable) release

QFeatures 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

QFeatures 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.

QFeatures 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

QFeatures 1.10

QFeatures 1.10.0

• New Bioconductor 3.17 (stable) release

QFeatures 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

QFeatures 1.8

QFeatures 1.8.0

• New Bioconductor 3.16 (stable) release

QFeatures 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.

QFeatures 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)

QFeatures 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)

QFeatures 1.2.0

QFeatures 1.2.0

• New release version (Bioc 3.13)

QFeatures 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

QFeatures 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