Changelog

Source: NEWS.md

QFeatures 1.5

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