Package split

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: cevomod
 Title: Cancer Evolution Models
-Version: 2.4.0
+Version: 3.0.0
 Authors@R: 
     person("Paweł", "Kuś", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-4367-9821"))
@@ -9,42 +9,34 @@ Description: Cancer Evolutionary Models. Set of methods facilitating the analysi
 License: GPL (>= 3)
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2
 Suggests: 
     BMix,
-    circlize,
-    ComplexHeatmap,
-    GenomicRanges,
-    ggrepel,
-    grid,
     mobster,
     mutSignatures,
     neutralitytestr,
     knitr,
-    patchwork,
-    pheatmap,
+    readthis,
     rmarkdown,
     shiny,
     shinydashboard,
     shinyWidgets,
     testthat (>= 3.0.0),
     tidyverse,
     vdiffr,
-    readthis,
     rsample,
     processx
 Config/testthat/edition: 3
 VignetteBuilder: knitr
 Imports: 
+    cevodata,
     cli,
     corrr,
     crayon,
     dplyr,
     forcats,
     ggplot2,
     mclust,
-    plyranges,
-    prismatic,
     progress,
     purrr,
     readr,
@@ -54,12 +46,15 @@ Imports:
     tibble,
     tidyr,
     tidyselect,
+    verbose,
     yardstick
 Depends: 
     R (>= 2.10)
 Remotes: 
     caravagnalab/mobster,
     caravagnalab/BMix,
-    pawelqs/readthis
+    pawelqs/cevodata,
+    pawelqs/readthis,
+    pawelqs/verbose
 LazyData: true
 URL: https://pawelqs.github.io/cevomod/, https://github.com/pawelqs/cevomod

NAMESPACE

@@ -1,173 +1,49 @@
 # Generated by roxygen2: do not edit by hand
 
-S3method("default_CNVs<-",cevodata)
-S3method("default_SNVs<-",cevodata)
-S3method(CNVs,cevodata)
-S3method(SNVs,cevodata)
-S3method(add_CNV_data,cevodata)
-S3method(add_SNV_data,cevodata)
-S3method(add_patient_data,cevodata)
-S3method(add_sample_data,cevodata)
-S3method(add_to_cevodata,cevo_ASCAT)
-S3method(add_to_cevodata,cevo_FACETS)
-S3method(add_to_cevodata,cevo_Mutect)
-S3method(add_to_cevodata,cevo_Strelka)
-S3method(calc_Mf_1f,cevo_snvs)
-S3method(calc_Mf_1f,cevodata)
-S3method(calc_SFS,cevo_snvs)
-S3method(calc_SFS,cevodata)
-S3method(calc_cumulative_tails,cevo_snvs)
-S3method(calc_cumulative_tails,cevodata)
-S3method(default_CNVs,cevodata)
-S3method(default_SNVs,cevodata)
-S3method(estimate_ITH,cevodata)
-S3method(filter,cevodata)
 S3method(fit_mobster,cevodata)
 S3method(fit_powerlaw_tail_fixed,cevodata)
 S3method(fit_powerlaw_tail_optim,cevo_SFS_bootstraps)
 S3method(fit_powerlaw_tail_optim,cevo_SFS_tbl)
 S3method(fit_powerlaw_tail_optim,cevodata)
-S3method(get_CNVs_var_names,cevodata)
-S3method(get_frequency_measure_name,cevo_snvs)
-S3method(get_frequency_measure_name,cevodata)
-S3method(get_model_names,cevodata)
-S3method(get_models,cevodata)
-S3method(get_mutation_rates,cevodata)
-S3method(get_mutation_rates,tbl_df)
-S3method(get_sample_mutation_burden,cevo_snvs)
-S3method(get_sample_mutation_burden,cevodata)
-S3method(get_sample_sequencing_depths,cevo_snvs)
-S3method(get_sample_sequencing_depths,cevodata)
-S3method(get_selection_coefficients,cevodata)
-S3method(get_selection_coefficients,tbl_df)
-S3method(intervalize_mutation_frequencies,cevo_snvs)
-S3method(intervalize_mutation_frequencies,cevodata)
-S3method(merge,cevodata)
-S3method(plot,cevo_ITH_tbl)
-S3method(plot,cevo_Mf_1f_tbl)
-S3method(plot,cevo_SFS_tbl)
-S3method(plot,cevo_cumulative_tails_tbl)
-S3method(plot_CNV_heatmap,cevodata)
-S3method(plot_ITH,cevodata)
-S3method(plot_Mf_1f,cevodata)
-S3method(plot_SFS,cevodata)
-S3method(plot_cumulative_tails,cevodata)
+S3method(get_evolutionary_parameters,cevodata)
+S3method(get_evolutionary_parameters,cv_powerlaw_models)
+S3method(get_evolutionary_parameters,cv_powerlaw_subclones_models)
 S3method(plot_models,cevodata)
-S3method(plot_mutations,cevodata)
-S3method(plot_mutations,tbl_df)
-S3method(plot_private_shared_mutations,cevodata)
-S3method(plot_sequencing_depth,cevo_snvs)
-S3method(plot_sequencing_depth,cevodata)
-S3method(print,cevo_palettes)
-S3method(print,cevo_snvs)
-S3method(print,cevodata)
-S3method(run_cevomod,cevodata)
-S3method(set_cancer_type,cevodata)
 S3method(shuffle,tbl_df)
-S3method(split_by,cevodata)
-S3method(summary,cevodata)
-S3method(update,cevodata)
 export("%not in%")
-export("default_CNVs<-")
-export("default_SNVs<-")
-export(CNVs)
-export(SNVs)
-export(SNVs_CNVs)
-export(active_models)
-export(add_CNV_data)
-export(add_SNV_data)
-export(add_data)
-export(add_patient_data)
-export(add_sample_data)
-export(add_to_cevodata)
-export(annotate_mutation_contexts)
-export(annotate_normal_cn)
-export(as_cevo_snvs)
 export(build_clip_container)
-export(calc_Mf_1f)
-export(calc_SFS)
-export(calc_cumulative_tails)
-export(calc_mutation_frequencies)
 export(compare_models)
-export(count_mutation_types)
+export(count_missing_powerlaw_tail_mutations)
 export(count_mutations_by_component)
-export(count_neutral_tail_filtered_mutations)
-export(count_neutral_tail_mutations)
-export(cut_f_intervals)
-export(default_CNVs)
-export(default_SNVs)
-export(dentro_2015_correction)
-export(estimate_ITH)
+export(count_powerlaw_tail_mutations)
 export(fill_na)
-export(filter)
-export(filter_SNVs_by_regions)
 export(fit_mobster)
 export(fit_powerlaw_tail_fixed)
 export(fit_powerlaw_tail_optim)
 export(fit_subclones)
 export(fit_subclones_bmix)
 export(fit_subclones_clip)
 export(fit_subclones_mclust)
-export(fix_powerlaw_N_mutations)
 export(generate_neutral_snvs)
 export(geom_powerlaw)
-export(get_CNVs_var_names)
-export(get_Mf_1f)
-export(get_SFS)
-export(get_SNVs_wider)
-export(get_cevomod_verbosity)
 export(get_containers_dir)
-export(get_frequency_measure_name)
-export(get_metadata)
-export(get_model_names)
-export(get_models)
-export(get_mutation_rates)
-export(get_patient_mutation_burden)
-export(get_residuals)
-export(get_sample_mutation_burden)
-export(get_sample_sequencing_depths)
-export(get_selection_coefficients)
-export(heatmap_granges)
-export(hide_facet_labels)
-export(hide_legend)
-export(impact_filter)
-export(init_cevodata)
-export(intervalize_mutation_frequencies)
+export(get_evolutionary_parameters)
+export(get_model_coefficients)
+export(get_model_residuals)
 export(layer_lm_fits)
-export(layer_mutations)
-export(plot_CNV_heatmap)
-export(plot_ITH)
-export(plot_Mf_1f)
 export(plot_Mf_1f_fits)
-export(plot_SFS)
 export(plot_binomial_fits_vs_powerlaw_residuals_bars)
-export(plot_cumulative_tails)
 export(plot_models)
-export(plot_mutations)
 export(plot_neutral_A_coefficients)
-export(plot_private_shared_mutations)
 export(plot_residuals_full_model)
 export(plot_residuals_powerlaw_model)
 export(plot_sampling_rate)
-export(plot_sequencing_depth)
-export(prepare_SNVs)
 export(quick_load)
 export(quick_save)
-export(rotate_x_labels)
 export(run_browser)
-export(run_cevomod)
-export(scale_color_cevomod)
-export(scale_fill_cevomod)
-export(set_cancer_type)
-export(set_cevomod_verbosity)
 export(set_containers_dir)
 export(shuffle)
-export(split_by)
-export(stat_cumulative_tail)
-export(to_clip)
-export(unite_mutation_id)
-export(use_purity)
-export(variant_classification_filter)
+import(cevodata)
 import(dplyr)
 import(forcats)
 import(ggplot2)

NEWS.md

@@ -1,3 +1,7 @@
+## cevomod 3.0.0
+* cevodata package extracted from the original cevomod
+* cevomod is now responsible only for fitting and plotting models and estimation
+  of evolutionary parameters
 
 ## cevomod 2.4.0
 * code clean-up, unnecessary dependencies removed
@@ -6,21 +10,18 @@
 * subclones can be fitted using [CliP](https://github.com/wwylab/CliP) [(Jiang et al., 2021)](https://www.biorxiv.org/content/10.1101/2021.03.31.437383v1) (`fit_subclones(method = "CliP")`). This option requires that the Apptainer is installed. CliP container image can be build with `build_clip_container()`
 
 ## cevomod 2.2.0
-* fit_powerlaw_tail_fixed() has a bootstrap option
+* fit_powerlaw_tail_fixed() has a bootstrap option. See the details in [Fitting models #Bootstrapping](https://pawelqs.github.io/cevomod/articles/fitting_models.html#bootstrapping) vignette.
 
 ## cevomod 2.1.0
 * cevomod is integrated with a helper [readthis](https://pawelqs.github.io/readthis/index.html) package, designed for bulk reading of variant files from algorithms such as Mutect2, Strelka, ASCAT, or FACETS, in the cevomod-friendly data format. Objects returned by `readthis::read_*()` functions can be added to the cevodata object using a general `add_data()` function.
 
-
 ## cevomod 2.0.0
 * cevomod functions can no utilize VAF or CCF (Cancer Cell Fraction) as a measure
   of mutation frequency. CCF is calculated using the formula introduced in [Dentro et al. *Principles of Reconstructing the Subclonal Architecture of Cancers* (2015)](https://doi.org/10.1101/cshperspect.a026625)
 
-
 ## cevomod 1.1.0
 * cevodata export to [CliP](https://github.com/wwylab/CliP) implemented
 
-
 ## cevomod 1.0.0
 * cevodata class implementation
 * fitting the power-law tails with exponent equal to 2 using $M(f) \sim 1/f$ statistic