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WTSI Mutational Signature Framework

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WTSI Mutational Signature Framework



23 Oct 2012 (Updated )

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

removeWeak(genomesOriginal, removeWeakMutationTypes)
function [genomes mutationTypesToRemoveSet] = removeWeak(genomesOriginal, removeWeakMutationTypes)

% Ludmil B. Alexandrov
% Cancer Genome Project
% Wellcome Trust Sanger Institute
% 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.

   [sortedTotalMutationTypes indexTotalMutationTypes] = sort(sum(genomesOriginal, 2), 'ascend');
   totalMutationTypes = sum(sum(genomesOriginal));
   totalMutatationTypesToRemove = sum(cumsum( sortedTotalMutationTypes )/ totalMutationTypes  < removeWeakMutationTypes);
   mutationTypesToRemoveSet = indexTotalMutationTypes(1:totalMutatationTypesToRemove);
   genomes = genomesOriginal;
   genomes(mutationTypesToRemoveSet, :) = [];

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