Changes in version 1.15 QFeatures 1.15.2 - 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