https://github.com/chrovis/clj-deconstruct-sigs

deconstructSigs for Clojure
https://github.com/chrovis/clj-deconstruct-sigs

clojure clojurescript cosmic mutational-signatures

Last synced: about 1 month ago
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deconstructSigs for Clojure

• Host: GitHub
• URL: https://github.com/chrovis/clj-deconstruct-sigs
• Owner: chrovis
• License: apache-2.0
• Created: 2019-01-31T06:51:23.000Z (almost 6 years ago)
• Default Branch: master
• Last Pushed: 2022-06-29T03:26:22.000Z (over 2 years ago)
• Last Synced: 2024-08-13T05:07:07.971Z (4 months ago)
• Topics: clojure, clojurescript, cosmic, mutational-signatures
• Language: Clojure
• Homepage:
• Size: 461 KB
• Stars: 4
• Watchers: 13
• Forks: 0
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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# clj-deconstruct-sigs

![Mutational Signature](docs/img/v3.2_SBS3_PROFILE_GA_GRCh37_ygeJJyb.original.jpg "Mutational Signature")

clj-deconstruct-sigs is a Clojure port of [deconstructSigs](https://github.com/raerose01/deconstructSigs).

## What are Mutational Signatures?

You can find a comprehensive description [here](https://cancer.sanger.ac.uk/cosmic/signatures).

In short, treating an individual's somatic mutation pattern as a combination of known distinct signatures could lead to insights of cancer's characteristics.

## Usage

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-names  - A map of weight that associated signature names as key on behalf of indices.

: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.

```clojure

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

;; A 96 element vector representing the substitution patterns as per https://cancer.sanger.ac.uk/cosmic/signatures.

;; 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 https://cancer.sanger.ac.uk/cancergenome/assets/signatures_probabilities.txt

(require '[clj-deconstruct-sigs.db])

(def cosmic-signatures (clj-deconstruct-sigs.db/load-signature-database "dev-resources/COSMIC_v3.2_SBS_GRCh38.txt"))

(which-signatures sample-tumor cosmic-signatures)

=>

{:seed-idx 25,

 :weights {0 0.36016636298023036,...},

 :weights-with-names {"SBS1" 0.36016636298023036,...},

 :product [6.690145741717268E-4,...],

 :unknown 0.09329024976612943,

 :diff [6.451870662289333E-4,...],

 :error-sum 0.023682681269721964}

```

## License

Copyright 2019-2022 [Xcoo, Inc.](https://xcoo.jp/)

Licensed under the [Apache License, Version 2.0](LICENSE).