region_cossim-class: An S4 class to store the results of a regional mutation...

In UMCUGenetics/MutationalPatterns: Comprehensive genome-wide analysis of mutational processes

An S4 class to store the results of a regional mutation pattern similarity analysis

Description

An S4 class to store the results of a regional mutation pattern similarity analysis

Slots

sim_tb

A tibble containing the calculated similarities of the windows.

pos_tb

A tibble containing the mutation positions.

chr_lengths

Vector containing the chromosome lengths.

window_size

The number of mutations in a window.

max_window_size_gen

The maximum size of a window before it is removed.

ref_genome

BSgenome reference genome object

muts_per_chr

Vector containing the number of mutations per chromosome.

mean_window_size

The mean length of the genome covered by the windows.

stepsize

The number of mutations that a window slides in each step.

extension

The number of bases, that's extracted upstream and downstream of the base substitutions, to create the mutation matrices.

chromosomes

Vector of chromosome/contig names of the reference genome to be plotted.

exclude_self_mut_mat

Boolean describing whether the mutations in a window should be subtracted from the global mutation matrix.

UMCUGenetics/MutationalPatterns documentation built on Nov. 24, 2022, 4:31 a.m.