Assign pre-calculated relative trinucleotide mutation rates
Source:R/set_trinuc_rates.R
set_trinuc_rates.RdThis 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.