set_trinuc_rates: Assign pre-calculated relative trinucleotide mutation rates

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

Assign pre-calculated relative trinucleotide mutation rates

Description

This function assigns trinucleotide-context-specific relative SNV mutation rates to tumors in a CESAnalysis. (These could be rates previously generated with trinuc_mutation_rates(), or they could calculated using your own methods.) The input rates must be a data.table or matrix. If supplying a data table, there must be a Unique_Patient_Identifier column; if supplying a a matrix, the identifiers should be supplied as rownames instead. Either way, all samples in the CESAnalysis must be represented in the input rates. To avoid user error, there cannot be any superfluous samples in the input rates unless ignore_extra_samples = T. Besides the identifier column (or matrix rownames), there must be 96 columns, with column names exactly matching the deconstructSigs/MutationalPatterns naming and order (run this function with incorrect column names, and the names you need to use will be printed). Since CES uses relative trinuc rates, rows must sum to 1, with all values greater than 0. You'll get a warning if any rate is less than 1e-9, since (unrealistically) low rates may crash selection model likelihood functions that aren't expecting such small values.

Usage

set_trinuc_rates(cesa, trinuc_rates, ignore_extra_samples = FALSE)

Arguments

cesa	CESAnalysis object
trinuc_rates	a matrix or data table (see description for format)
ignore_extra_samples	skip samples in the input table that are not in the CESAnalysis (when false, will stop with an error)

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