I'm currently using SomaticSignatures package to extract signatures from my NGS datas.
I wanted to compare it to validated mutational signatures published by Alexandrov et al. (ALEXANDROV, Ludmil B., NIK-ZAINAL, Serena, WEDGE, David C., et al. Signatures of mutational processes in human cancer. Nature, 2013.) , to evaluate the implication of each validated profile in my datas.
I got their profiles on their server (ftp://ftp.sanger.ac.uk/pub/cancer/AlexandrovEtAl) and included them in the matrix obtained from mutationContextMatrix function (= sca_occurence in tutorial).
Then I applied the 3 statistical methods (nmf, pca and kmeans). But the tool pools and calculates again all the mutational profiles.
Is there a method to fix validated profiles and just having an estimation of their implication in my datas?