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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_epistasis()
Plot pairwise epistasis
plot_signature_effects()
Plot mutational source and effect attributions

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