SBS_mm9.data.frame as input object for sig in get_sig_similarity() and sig_fit().g_label option in show_group_distribution() to better control group names.test option and variable checking in show_cor().output_sig() to output signature exposure distribution (#280).show_cor() for general association analysis.show_group_distribution() to control segments.add_labels(), thanks to TaoTao for reporting., seperated indices in show_cosmic_signatures.set_order in get_sig_similarity() (#274).output_sig().show_sig_bootstrap_error(), now it is “Reconstruction error (L2 norm)”auto_reduce option in sig_fit* functions to improve signature fitting.sig_fit().sig_auto_extract() to ‘optimal’.get_sig_cancer_type_index().sigprofiler_extract() to reduce failure in when refit is enabled.output_sig().show_group_distribution().optimize option in sig_extract() and sig_auto_extract()., in sig_fit() and sig_fit_bootstrap* functions.output_* functions from sigflow.sig_tally().highlight_genes in show_cn_group_profile() to show gene labels.get_sig_cancer_type_index() to get reference signature index.show_group_distribution() to show group distribution.show_cn_profile() to show specified ranges and add copy number value labels.nnls instead of pracma for NNLS implementation in sig_fit().BSgenome.Hsapiens.1000genomes.hs37d5 in sig_tally().MT to M in mutation data.show_sig_exposure().letter_colors as an unexported discrete palette.transform_seg_table().show_cn_group_profile().show_cn_freq_circos().sig_orders option in show_sig_profile() function now can select and order signatures to plot.show_sig_profile_loop() for better signature profile visualization.read_copynumber(), got 200% improvement.read_copynumber(), got 20% improvement.cosine() function.get_sig_db() to let users directly load signature database.sigprofiler_extract() and sigprofiler_import() to call SigProfiler and import results.read_vcf() for simply reading VCF files.show_sig_profile_heatmap().read_copynumber_seqz() to read sequenza result directory.read_copynumber().read_maf().sig_fit() to ‘NNLS’ and implement it with pracma package (#216).use_all option in read_copynumber() working correctly.MRSE to RMSE.show_sig_bootstrap_*() for plotting aggregated values.get_groups() for clustering.highlight_size for show_sig_bootstrap_*().sig_fit() function to better visualize a few samples.lsei package was removed from CRAN, here I reset default method to ‘QP’ and tried best to keep the LS usage in sigminer (#189).show_sig_profile() and added input checking for this function.furrr, solution is from https://github.com/DavisVaughan/furrr/issues/107.sig_fit() for methods QP and SA.show_sig_fit() and show_sig_bootstrap_* functions.sig_fit_bootstrap_batch for more useful in practice.show_groups() to show the signature contribution in each group from get_groups().get_groups() to result of sig_fit().sig_fit_bootstrap_batch().sig_tally().cores > 1 (#161).sig_fit().sig_fit_bootstrap() for bootstrap results.Imports to Suggests.report_bootstrap_p_value() to report p values.data().fuzzyjoin package from dependency.ggalluvial package to field suggsets.All users, this is a break-through version of sigminer, most of functions have been modified, more features are implemented. Please read the reference list to see the function groups and their functionalities.
Please read the vignette for usage.
I Hope it helps your research work and makes a new contribution to the scientific community.