baseline_mutation_rates: Baseline mutation rate calculation

In Townsend-Lab-Yale/cancereffectsizeR: Calculate Cancer Effect Size

Baseline mutation rate calculation

Description

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.

Value

a data table of mutation rates with one column per variant, and a Unique_Patient_Identifier column identifying each row

Townsend-Lab-Yale/cancereffectsizeR documentation built on April 28, 2024, 6:14 p.m.