Skip mutational signature analysis and assign group average relative trinucleotide-context-specific mutation rates to all samples
Source:R/assign_group_average_trinuc_rates.R
assign_group_average_trinuc_rates.RdThis function calculates the relative rates of trinucleotide-context-specific mutations across all SNV records from whole-exome and whole-genome MAF data and naively assigns these rates to all samples. This can be helpful if you do not have SNV mutational signatures available for your species, or if you want to assume that all samples share the same SNV mutational processes without relying on signatures. Normally, if mutational signatures are available, it is better to use trinuc_snv_mutation_rates().
Details
To reduce the influence of selection, only non-recurrent mutations (i.e., mutations that occur in just one sample) are used to calculate the rates. Targeted sequencing data is excluded for the same reason, and also because the trinucleotide composition of targeted regions could be very different from that of the exome/genome.