Function reference • cevomod

cevodata

as_cevo_snvs(): Create cevo_snvs tibble

init_cevodata(): Create new cevomod dataset object

add_SNV_data() add_CNV_data() SNVs() get_SNVs_wider() CNVs(): Get/Add SNV/CNV data from the cevodata dataset

add_patient_data() add_sample_data(): Add metadata to the cevodata object

add_data() add_to_cevodata(): readthis integration

default_SNVs() `default_SNVs<-`() default_CNVs() `default_CNVs<-`(): Get/Set active assays of the cevodata object

set_cancer_type(): Set cancer type for the object

use_purity(): Choose purity measure

cevodata transformations

filter(<cevodata>): Filter/subset cevodata object

split_by(): Split object

merge(<cevodata>): Merge two cevodata objects

update(<cevodata>): Update cevodata object with values from another object

Other transformations

annotate_mutation_contexts(): Annotate mutation context and types for mutation signatures analysis

unite_mutation_id(): Unite many columns to create mutation_id column

cut_f_intervals(): Get mutation frequency intervals

filter_SNVs_by_regions(): Filter SNVs by position: using regions tbl or bed file

shuffle(): Shuffle order of elements in object

Data preparation

annotate_normal_cn(): Annotate chromosome ploidies in CNV data

calc_mutation_frequencies() dentro_2015_correction(): Calc mutation frequencies

intervalize_mutation_frequencies(): Intervalize the mutation frequencies

prepare_SNVs(): Prepare SNVs for analyses

Model fitting

fit_mobster(): Fit Mobster models

fit_subclones() fit_subclones_bmix() fit_subclones_clip() fit_subclones_mclust(): Fit clonal and subclonal components of the model to the residuals of the power-law model

fit_powerlaw_tail_fixed() layer_lm_fits(): Fitting neutral models

fit_powerlaw_tail_optim(): Fitting power-law tails with aptimum exponent value

Getters

calc_Mf_1f() plot_Mf_1f() get_Mf_1f(): William's M(f) ~ 1/f statistics

add_SNV_data() add_CNV_data() SNVs() get_SNVs_wider() CNVs(): Get/Add SNV/CNV data from the cevodata dataset

get_mutation_rates() get_selection_coefficients(): Get evolutionary parameters from the model

get_CNVs_var_names(): Get names of CNV variables

get_cevomod_verbosity(): Get the verbosity level

get_frequency_measure_name(): Decide which mutation frequency measure to use

get_metadata(): Get sample metadata

get_model_names(): Get model names

get_models(): Get models from the object

get_patient_mutation_burden(): Get tumor mutation burden

get_residuals(): Get model residuals

get_sample_mutation_burden(): Get sample mutation burden

get_sample_sequencing_depths(): Get sample sequencing depths

set_containers_dir() get_containers_dir(): Get/Set the containers directory

calc_SFS() plot_SFS() get_SFS(): Site Frequency Spectra

active_models(): Get the name of the active models

SNVs_CNVs(): Get SNVs with merged CNVs

Evolutionary parameters

get_mutation_rates() get_selection_coefficients(): Get evolutionary parameters from the model

Visualizations

compare_models(): Compare fits from many models

geom_powerlaw(): Plot power-law curve

hide_facet_labels(): Hide facet labels

hide_legend(): Hide legend

plot_mutations() layer_mutations(): Show mutations in particular genes

fit_powerlaw_tail_fixed() layer_lm_fits(): Fitting neutral models

plot_ITH() plot(<cevo_ITH_tbl>) estimate_ITH(): Intratumor heterogeneity

calc_Mf_1f() plot_Mf_1f() get_Mf_1f(): William's M(f) ~ 1/f statistics

plot_CNV_heatmap() heatmap_granges(): Plot CNV heatmap

calc_cumulative_tails() plot_cumulative_tails(): Cumulative tails

plot(<cevo_Mf_1f_tbl>): Plot M(f) ~ 1/f

plot(<cevo_SFS_tbl>): Plot SFS

plot(<cevo_cumulative_tails_tbl>): Plot the cumulative tails

plot_Mf_1f_fits(): Plot M(f) ~ 1/f fits

plot_models(): Plot cevodata models

plot_neutral_A_coefficients(): Plot 'a' coefficients for all fitted neutral models

plot_private_shared_mutations(): Plot proportions of private and shared mutations

plot_sampling_rate() plot_residuals_powerlaw_model() plot_residuals_full_model() plot_binomial_fits_vs_powerlaw_residuals_bars(): Plot model residuals

plot_sequencing_depth(): Plot sequencing depth of cevodata

calc_SFS() plot_SFS() get_SFS(): Site Frequency Spectra

rotate_x_labels(): Rotate x axix labels

scale_fill_cevomod() scale_color_cevomod(): Different color pallettes

stat_cumulative_tail(): Plot Cumulative Tail

Data

driver_genes: Tbl of driver genes from Bailey, Ding et al. 'Comprehensive Characterization of Cancer Driver Genes and Mutations', Cell, 2-18 https://doi.org/10.1016/j.cell.2018.02.060

test_data: 4 test samples

test_data_fitted: cevomod results for 4 test samples

Other functions

build_clip_container(): Build the CliP Apptainer container

fill_na(): Fill na values in the object

fix_powerlaw_N_mutations(): Fill N_mutations column for powerlaw models

generate_neutral_snvs(): Generate neutral SNVs

set_cevomod_verbosity(): Change the verbosity level

set_containers_dir() get_containers_dir(): Get/Set the containers directory

to_clip(): Export cevodata to CliP input

`%not in%`: Not in operator