Preparing for Bioconductor release. We address comments from Bioconductor reviewers. Major changes include parameter validation and vectoriation of functions. filter_mut() "snv_in_germ_mnv" parameter was fixed such that it now only filters out overlapping snvs if their variation matches that of the germline mnv (previously it was blanket removing all snvs that overlap with germline mnvs). plot_lollipop() can now colour the plot by different subtype resolutions (previously just base_6). Fixed plot_spectra() axes labels after clustering (previously not showing labels).
Fix dependencies for Bioconductor release.
Preparing for Bioconductor release. This change removes bmd_toxicR from the package. ToxicR dependency is not supported by Bioconductor. See ToxicR_archive branch for bmd_toxicr function. Modifies signature_fitting() to use SigProfilerMatrixGenerator python dependency rather than R dependency.
Preparing for Bioconductor release. This change adds MutSeqRData to suggests, and alters how the examples are run (now depends on the ExperimentHub accessions).
Initial public version.
filter_mut() to workflow: germline identification via vaf_cutoff, region filtering, and depth correction now occur here instead of the import functions.calculate_mut_freq() is renamed to calculate_mf().calculate_mf() no longer requires depth; users may:
correct_depth option moved to calculate_mf().plot_spectra(), plot_trinucleotide(), and spectra_comparison() now use mf_data instead of raw mutations.render_report() added for standardized summary reporting.custom_regions parameter; replaced by generalized regions argument.