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Mutational Signature

clj-deconstruct-sigs is a Clojure port of deconstructSigs.

What are Mutational Signatures?

A comprehensive description can be found here. In short, treating an individual's somatic mutation pattern as a combination of known distinct signatures could lead to insights of cancer's characteristics.


The main function is clj-deconstruct-sigs.core/which-signatures, which takes a sample tumor and a reference signatures matrix and returns a map with the following keys.

:seed-idx - Index of the signature that was used as the initial seed
:weights  - A map of weight indices to weight. :weights* with zero contribution entries
:weights* - A map of non-zero weight indices to weight. Note that entries that have zero contribution will be missing.
:product - matrix product of :weights and the provided signatures
:unknown - 1 minus the sum of weights
:diff - element wise difference of the provided sample tumor and the product
:error-sum - Square root of the sum of the element wise square of :diff. Indicates how close the :product is from the original input

Here is a repl session that adds more context.

(require '[clj-deconstruct-sigs.core :refer :all])

;; A 96 element vector representing the substitution patterns as per
;; Start from A[C>A]A and ends with T[T>G]T
(def sample-tumor [0.00131420164040066,....])

;; Reference set of signatures to use, represented with m rows x 96 columns.
;; This library provides cosmic.signature-data.generated/latest-cosmic-signatures which is based on parsing the latest
;; signatures at
(require '[])

(which-signatures sample-tumor
{:seed-idx 25,
 :weights {7 0.36016636298023036,...},
 :weights* {0 0.0, ...},
 :product [6.690145741717268E-4,...],
 :unknown 0.09329024976612943,
 :diff [6.451870662289333E-4,...],
 :error-sum 0.023682681269721964}


Copyright 2019 Xcoo, Inc.

Licensed under the Apache License, Version 2.0.

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