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NAMESPACE
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NAMESPACE
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# 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(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_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(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(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(dplyr)
import(forcats)
import(ggplot2)
import(purrr)
import(readr)
import(stringr)
import(tibble)
import(tidyr)
importFrom(mclust,mclustBIC)
importFrom(progress,progress_bar)
importFrom(rlang,":=")
importFrom(rlang,.data)
importFrom(rlang,.env)
importFrom(stats,sd)
importFrom(tidyselect,where)
importFrom(yardstick,rsq_vec)