Changelog

Source: NEWS.md

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