v1.2.0 development PR #20
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Updated implementation of unit tests to capture messages and errors and split testing into smaller units within single file
Added external script to generate example data for each class and method used in the package for quick loading and use in testing and documented examples
Updated plotActivities to set input as NULL if not specified
Added unit testing for plotActivites to meet reasonable code coverage
No code just file to contain the tests for plotSegment
Added testing for getSamples and getSamplefeatures
Added getSampleByComponent testing using testthat
Added tests for user-facing "get" methods
Added testthat testing for scaleByModel using independent data, testing for clinPredictionPlatinum and depreciated clinPredictionDenovo as it does not function as intended.
Implemented testing for ClinPredictDenovo and depreciated. Added testing for getPloidyfeat, getSegCounts, and avoidMeasurementErrors. Added testing for addSampleFeatures and improved data.frame merging to return only samples present in object rather than all available rows in sample.feature data. Fixed requirement for all samples to match between data sets to only require one match.
Improved and fixed data input where header does not match expected input or includes columns in addition to the required columns. Adds reordering to ensure columns are in the correct order.
Completed depreciation of clinPredictionDenovo function and updated associated examples, vignette calls, and return value.
Added testing units for CNQuant and SigQuant subsetting functions
Added test for idSmoothingTargets function
Fixed a bug where specifying a single core resulted in a different computation of components and signatures due to a missing argument on an internal function. Calculation now correctly removes normal segments - rerunning signature extraction is recommended.
Added error catch to warn and prevent errors when no samples have sufficient seg counts to calculate copy number signatures
Computation of nSamp was using full sample set not filtered sample set - impact is minimal as step is partially redundant but caused edge case bug in GEL implementation.
Added functionality to report and add metadata to sample features for samples with too few non-diploid segments. Added parameter to specify non-diploid segment threshold. Removed unassigned use of SMOOTHINGFACTOR.
Fixed a bug in which CNSig class object initialisation date was fixed on package load rather than object instance creation. Added method to check and set column type for segTable input. Refactored createCNQuant to remove replicate code block.
Updated version number for dev to main PR
Refactored code comparing class identity to resolve build check warning. Commented out redundant class comparison lines related to QDNAseq class objects which are handled beforehand.
Updated the description to remove unnecessary import of default packages `base` and `parallel`, the namespaces of which were not called, to resolve a R build warning.
Regenerate example class objects to remove activity errors caused by inclusion of normal segments due to bug in single vs multicore implementation.
Added additional testing line in example_data.R file used for development testing.
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PR for dev branch