assign_group_average_trinuc_rates: Skip mutational signature analysis and assign group average...

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

Skip mutational signature analysis and assign group average relative trinucleotide-context-specific mutation rates to all samples

Description

This 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().

Usage

assign_group_average_trinuc_rates(cesa)

Arguments

cesa	CESAnalysis object

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.

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