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WTSI Mutational Signature Framework

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WTSI Mutational Signature Framework

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23 Oct 2012 (Updated )

Framework for deciphering signatures of mutational processes from a set of mutational catalogues

example4.m
%% Example for deciphering mutational signatures with strand bias
%% when the number of signatures is KNOWN
%
% Ludmil B. Alexandrov
% Cancer Genome Project
% Wellcome Trust Sanger Institute
% la2@sanger.ac.uk
%
% This software and its documentation are copyright 2012 by the
% Wellcome Trust Sanger Institute/Genome Research Limited. All rights are reserved.
% This software is supplied without any warranty or guaranteed support whatsoever. 
% Neither the Wellcome Trust Sanger Institute nor Genome Research Limited 
% is responsible for its use, misuse, or functionality.

clear all;
addpath('source/');
addpath('plotting/');
clc;

%% Open matlabpool
if ( matlabpool('size') == 0 )
    matlabpool open; % opens the default matlabpool, if it is not already opened
end

%% Define parameters 
totalSignatures = 2;
iterationsPerCore = 10;
inputFile = 'input/100_WTSI_BRCA_whole_exome_substitutions_strand_bias.mat';
outputFile = 'output/res_example_4_100_WTSI_BRCA_whole_exome_substitutions_strand_bias.mat';

%% Decipher the signatures of mutational processes from catalogues of mutations
[input allProcesses allExposures idx processes exposures processStab processStabAvg] = ...
    decipherMutationalProcesses(iterationsPerCore, totalSignatures, inputFile, outputFile);

%% Plotting the signatures of mutational processes
plotSignaturesWithStrandBias(processes, allProcesses, idx, input);

%% Plotting the signature exposures
plotSignaturesExposureInSamples(exposures, input);

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