NEWS
notame 1.1.0
New features
- All feature data columns that differ between batches are now retained when merging batches: the most common flag value across batches is included in the "Flag" column in the merged object
- Added function 'read_from_msdial()' which reads MS-DIAL output files (tab-separated .txt files) into a SummarizedExperiment object
- Improved type conversion when importing data with notame functions
Bug fixes
- Fixed an issue where metadata was not properly retained when joining new data with join_rowData() and join_colData()
notame 1.0.0
- split notameViz and notameStats from notame
- removed MetaboSet-support
- included SummarizedExperiment-support
- parallelization with BiocParallel
- included website with rworkflows (reference index and vignette also cover notameViz and notameStats)
- removed perform_pairwise_t_test() and perform_paired_t_test(), replaced by perform_t_test()
- removed perform_pairwise_non_parametric() and perform_wilcoxon_signed_rank(), replaced by perform_non_parametric()
- removed align_batches(), replaced by batchCorr::alignBatches()
- removed normalize_batches(), replaced by batchCorr::normalizeBatches()
- other removed functions: install_dependencies(), merge_exprs(), plot_sample_suprahex(), prop_found(), prop_na(), finite helpers such as finite_mean() and simple transformations such as exponential()
- removed plotting in correct_drift(), replaced by save_dc_plots()
- removed plotting in cluster_features(), replaced by visualize_clusters()
- de-exported low-level functionality for drift correction and feature clustering
- renamed read_from_excel() to import_from_excel()
- renamed clean_stats_results() to summarize_results()
- renamed visualizations() to save_QC_plots()
- renamed merge_objects() to merge_notame_sets()
- renamed example_set to toy_notame_set and removed other example data
- reworked vignettes
- reworked plotting functionality in mixOmics_pls() and other mixOmics wrappers
- updated flag_contaminants to use whole number instead of ratio in threshold and include more metrics to flag by
- updated muvr_analysis() to use MUVR2 instead of MUVR package
notame 0.99.0
- submitted to Bioconductor