Package index • tickTack

All functions

CNA(): Extract CNAs.

Mutations(): Extract mutations.

add_DP_and_NV(): add_DP_and_NV Function

add_drivers_to_segment_plot(): Add driver mutation annotations to a segment plot

chr_coordinates_GRCh38: GRCh38 coordinates

chr_coordinates_hg19: hg19 coordinates

convert_name(): Convert model names to standardized names

convert_to_granges(): convert_to_granges Function

fit(): Fit timing of clonal peaks in cancer genome sequencing data

fit_h(): Get the fit to obtain the clocks posteriors

fit_h_single_k(): Get the fit to obtain the clocks posteriors

fit_variational_h(): fit_variational Function

get_clonal_peaks(): get_clonal_peaks Function

get_drivers(): Extract driver mutations from mutation data

get_initialization(): get_initialization

get_k_max_k_means(): model_selection Function

get_major(): get_major Function

get_reference(): Get reference genome coordinates

get_simulation(): get_simulation Function

get_simulation_tickTack(): get_taus_karyo Function

get_taus_karyo(): get_taus_karyo Function

get_taus_karyo_gerstrung(): get_taus_karyo gerstrung

has_driver_data(): Check if mutation data has driver annotations

karyo_to_int(): karyo_to_int Function

model_selection_h(): model_selection Function

pcawg_example: pcawg_example

pcawg_example_2: pcawg_example_2

plot_cnaqc(): Plot

plot_elbo_h(): Plot elbo Function

plot_model_selection_h(): Plot the behavior of the model selection scores vs the number of clusters

plot_posterior_clocks_h(): Plot posterior clocks distributions obtained from the hierarchical model fit

plot_posterior_weights_h(): Plot posterior weights distributions obtained from the hierarchical model fit

plot_segments_tick_tack(): Plot segmentation results from tickTack analysis

plot_segments_tick_tack_CN(): Plot copy number segments from CNAqc

plot_segments_tick_tack_data(): Plot mutation data from tickTack analysis

plot_timing(): Plot timing of clonal peaks in cancer genome sequencing data

plot_timing_h(): plot_timing_h Function

plot_vaf(): Plot variant allele frequency (VAF) distributions

prepare_input_data(): prepare_input_data Function

simulate_mutations(): simulate_mutations Function