Package index • cancereffectsizeR

Create and manage projects

Create, load, and save projects

CESAnalysis(): Create a cancereffectsizeR analysis

load_cesa(): Load a previously saved CESAnalysis

save_cesa(): Save a CESAnalysis in progress

set_refset_dir(): Set reference data directory

Obtain and prep MAF data

preload_maf(): Read and verify MAF somatic mutation data

check_sample_overlap(): Catch duplicate samples

get_TCGA_project_MAF(): Get MAF data from TCGA cohort

vcfs_to_maf_table(): Read a VCF into an MAF-like table

make_PathScore_input(): Make a PathScore input file from MAF data

lift_bed(): Convert BED intervals between genome builds

Load and manage variants

load_maf(): Load MAF somatic mutation data

select_variants(): Select and filter variants

variant_counts(): Assess variant prevalence and coverage

samples_with(): Find samples with specified variants

add_variants(): Add variant annotations

add_covered_regions(): add_covered_regions

baseline_mutation_rates(): Baseline mutation rate calculation

Load sample-level data

load_sample_data(): Add sample data

clear_sample_data(): Clear sample data

Compound variants

Combine variants into arbitrary batches and test for batch-level selection

define_compound_variants(): Divide batches of variants into a CompoundVariantSet

CompoundVariantSet(): Create CompoundVariantSet from variant IDs

Trinucleotide signatures and rates

Mutational signature extraction and inference of context-specific mutation rates

trinuc_mutation_rates(): Calculate relative rates of trinucleotide-context-specific mutations by extracting underlying mutational processes

suggest_cosmic_signature_exclusions(): Tissue-specific mutational signature exclusions

trinuc_snv_counts(): Tabulate SNVs by trinucleotide context

convert_signature_weights_for_mp(): Get MutationalPatterns contributions matrix

clear_trinuc_rates_and_signatures(): Clear mutational signature attributions and related mutation rate information

set_signature_weights(): Set SNV signature weights

set_trinuc_rates(): Assign pre-calculated relative trinucleotide mutation rates

assign_group_average_trinuc_rates(): Skip mutational signature analysis and assign group average relative trinucleotide-context-specific mutation rates to all samples

Gene mutation rates

Calculate neutral gene mutation rates

gene_mutation_rates(): Use dNdScv with tissue-specific covariates to calculate gene-level mutation rates

set_gene_rates(): Assign pre-calculated regional mutation rates

clear_gene_rates(): Clear regional mutation rates

Cancer effect sizes

Quantify selection for somatic variants

ces_variant(): Calculate cancer effects of variants

ces_epistasis(): Variant-level pairwise epistasis

ces_gene_epistasis(): Gene-level epistasis

mutational_signature_effects(): Attribute cancer effects to mutational signatures

clear_effect_output(): Clear variant effect output

clear_epistasis_output(): Clear epistasis output

Visualization

Display and compare variant effect sizes

plot_effects(): Plot cancer effects

plot_signature_effects(): Plot mutational source and effect attributions

plot_epistasis(): Plot pairwise epistasis

epistasis_plot_schematic(): Get epistatic effect schematic

Selection models

Likelihood function generators for various models of selection

sswm_lik(): sswm_lik

pairwise_epistasis_lik(): pairwise_epistasis_lik

Explore reference data

cosmic_signature_info(): Get COSMIC signature descriptions

get_PathScore_coding_regions(): Get PathScore coding regions

list_ces_refsets(): list_ces_refsets

list_ces_covariates(): list_ces_covariates

list_ces_signature_sets(): list_ces_signature_sets

get_ces_signature_set(): get_ces_signature_set

Create custom reference data

Build your own reference data set for almost any genome or tissue type

create_refset(): Create a custom refset

build_RefCDS(): cancereffectsizeR's RefCDS builder

validate_signature_set(): validate_signature_set

Accessors

Data accessors that you probably won’t need (use cesa$maf, cesa$samples, etc. instead)

maf_records(): View data loaded into CESAnalysis

excluded_maf_records(): View excluded MAF data

get_sample_info(): View sample metadata

get_trinuc_rates(): Get estimated relative rates of trinucleotide-specific SNV mutation

get_signature_weights(): Get table of signature attributions

get_gene_rates(): Get table of neutral gene mutation rates

snv_results(): View results from ces_variant

epistasis_results(): View output from epistasis functions