readAlexandrovSignatures {decompTumor2Sig} | R Documentation

## Read Alexandrov-type signatures (COSMIC format).

### Description

'readAlexandrovSignatures()' reads a set of Alexandrov-type signatures (COSMIC format) from a flat file or URL. Signatures must be specified in the tab-separated format used by the COSMIC website; see details below or
http://cancer.sanger.ac.uk/cosmic/signatures -> "Download signatures".

### Usage

    readAlexandrovSignatures(file)

### Arguments

`file` | (Mandatory) Can be a file name or an URL for download. Default (COSMIC): "https://cancer.sanger.ac.uk/cancergenome/assets/signatures_probabilities.txt"

### Details

COSMIC format for Alexandrov signatures:

Subst. | Trinucleotide | Mutation Type | Signature 1 | Signature 2 | ...
C>A | ACA | A[C>A]A | 0.0110983262 | 0.0006827082 | ...
C>A | ACC | A[C>A]C | 0.0091493407 | 0.0006191072 | ...
C>A | ACG | A[C>A]G | 0.0014900705 | 0.0000992790 | ...
C>A | ACT | A[C>A]T | 0.0062338852 | 0.0003238914 | ...
[...]
T>G | TTG | T[T>G]G | 0.0020310769 | 0.0002066152 | ...
T>G | TTT | T[T>G]T | 0.0040301281 | 0.0000235982 | ...

### Value

A list of Alexandrov signatures that can be used for `decomposeTumorGenomes`.

### Author(s)

Rosario M. Piro
Freie Universitaet Berlin
Maintainer: Rosario M. Piro
E-Mail: <rmpiro@gmail.com> or <r.piro@fu-berlin.de>

### References

http://rmpiro.net/decompTumor2Sig/
Krueger, Piro (2018) decompTumor2Sig: Identification of mutational signatures active in individual tumors. BMC Bioinformatics (accepted for publication).
Krueger, Piro (2017) Identification of Mutational Signatures Active in Individual Tumors. NETTAB 2017 - Methods, Tools & Platforms for Personalized Medicine in the Big Data Era, October 16-18, 2017, Palermo, Italy. PeerJ Preprints 5:e3257v1, 2017.

### See Also

`decompTumor2Sig`
`readShiraishiSignatures`

### Examples

    ### get Alexandrov signatures from COSMIC
    signatures <- readAlexandrovSignatures()

[Package decompTumor2Sig version 2.0.0 Index]