From the 2nd to the last column show the value of mutation features. The 5th colum shows the alternate base (A, C, G, or T). The 4th column shows the reference base (A, C, G, or T). The 3rd column shows the coordinate in the chromosome. The 2nd column shows the name of chromosome. The 1st column shows the name of samples. 5’ and 3’ flanking bases (A, C, G and T)Ĭurrently, pmsignature can accept following two formats of tab-delimited text file. 6 substitutions (C>A, C>G, C>T, T>A, T>C and T>G). Here, mutation features are elements used for categorizing mutations such as: A simple model-based approach to inferring and visualizing cancer mutation signatures, PLoS Genetics, 2015, 
pmsignature provides intuitively interetable visualization of mutation signatures, which is analogous to sequencing logos.
pmsignature can perform robust estimation of mutation signatures in case of many contextual factors are taken into account such as two bases 5' and 3' to the mutated sites.Principal component analysis or nonnegative matrix factorization have been popular.Ĭompared to these existing approaches, the pmsignature has following advantages: For efficiently extracting characteristic mutation patterns (mutation signatures)įrom the set of mutations collected typically from cancer genome sequencing data.
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