Calculates neutral mutation rates at specific sites based on gene mutation rates and the relative trinucleotide-context-specific SNV mutation rates of each sample
Usage
baseline_mutation_rates(
cesa,
aac_ids = NULL,
snv_ids = NULL,
variant_ids = NULL,
samples = character()
)Arguments
- cesa
CESAnalysis with gene mutation rates and tumor-specific trinucleotide-context-specific mutation rates already calculated
- aac_ids
vector of IDs for amino acid change variants
- snv_ids
vector of IDs for SNVs
- variant_ids
vector of mixed IDs (faster to use snv_ids and aac_ids for large jobs, if already known)
- samples
Which samples to calculate rates for. Defaults to all samples. Can be a vector of Unique_Patient_Identifiers, or a data.table containing rows from the CESAnalysis sample table.