pull request - feature updates v1.1.0 #13
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Added function framework and data sets for specification of cancer-specific Signature definition subsets defined by Drews. Provides ground work for use of denovo signature discovery mapping.
Implementation of method to check chromosome format to ensure consistency. Formats including "chr", numeric sex chromosomes, or additional non-ref contigs.
Implementation of a generic function to extract the copy number signatures matrix from a SigQuant object without directly accessing the structure.
Renamed getSignature function to getActivities to maintain naming consistency
setup testthat for package testing framework
Added a function to retrieve the extracted copy number features from a CNQuant object without needing to access the slots directly.
Regenerated and implemented proper data formats for example data used in vignettes and code examples to be loaded via `data()`. Added a data-raw folder to contain code used to generate cancer-specific signature data
Added empty featData slot error catch for function getFeatures()
Overhaul of the class and generic function documentation. Including better descriptions of usage, parameters, linking between functions and classes. Includes update to used roxygen2 version. Addition of example datasets as properly implemented datasets. Fixed license file naming. Added single testthat example.
Documentation overhaul for non-generic and non-class functions. Improved arguments and parameterisation for plotting functions.
Update release version to match github release version.
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dev build for version 1.1.0 - continued commits needed