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 for signatures version 2 (March 2015), the comma-separated format used for signatures version 3 (May 2019), the Microsoft Excel 2007+ sheet used for version 3.1, or the tab-sperated format used for version 3.2 (see Details below). Excel sheets cannot be read from an URL and must be downloaded first.

### Usage

    readAlexandrovSignatures(file)

### Arguments

`file` | (Mandatory) Can be a file name or an URL for download. Default: "https://cancer.sanger.ac.uk/cancergenome/assets/signatures_probabilities.txt" (COSMIC signatures v2).

### Details

For details on the accepted signature formats, see below or
http://cancer.sanger.ac.uk/cosmic/signatures_v2 -> "Download signatures" for version 2,
https://www.synapse.org/#!Synapse:syn12009743 for version 3,
https://cancer.sanger.ac.uk/sigs-assets-20/COSMIC_Mutational_Signatures_v3.1.xlsx for version 3.1,
and https://cancer.sanger.ac.uk/signatures/ for version 3.2. For versions 3, 3.1 and 3.2, only Single Base Substitution (SBS) signatures can be used.

COSMIC format for Alexandrov signatures, version 2:

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 | ...

COSMIC/Synapse format for Alexandrov signatures, version 3 and 3.1:

Type,SubType,SBS1,SBS2,SBS3,SBS4,SBS5,SBS6, ...
C>A,ACA,8.86E-04,5.80E-07,2.08E-02,4.22E-02,1.20E-02,4.25E-04, ...
C>A,ACC,2.28E-03,1.48E-04,1.65E-02,3.33E-02,9.44E-03,5.24E-04, ...
C>A,ACG,1.77E-04,5.23E-05,1.75E-03,1.56E-02,1.85E-03,5.20E-05, ...
C>A,ACT,1.28E-03,9.78E-05,1.22E-02,2.95E-02,6.61E-03,1.80E-04, ...
[...]
T>G,TTG,5.83E-04,9.54E-05,8.05E-03,2.32E-03,6.94E-03,3.24E-04, ...
T>G,TTT,2.23E-16,2.23E-16,1.05E-02,5.68E-04,1.35E-02,1.01E-03, ...

Version 3.1 has assentially the same format as version 3, but is distributed as an Excel spread sheet.

COSMIC/Synapse format for Alexandrov signatures, version 3.2:

Type | SBS1 | SBS2 | ...
A[C>A]A | 0.0110983262 | 0.0006827082 | ...
A[C>A]C | 0.0091493407 | 0.0006191072 | ...
A[C>A]G | 0.0014900705 | 0.0000992790 | ...
A[C>A]T | 0.0062338852 | 0.0003238914 | ...
[...]
T[T>G]G | 0.0020310769 | 0.0002066152 | ...
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
Politecnico di Milano
Maintainer: Rosario M. Piro
E-Mail: <rmpiro@gmail.com> or <rosariomichael.piro@polimi.it>

### References

http://rmpiro.net/decompTumor2Sig/
Krueger, Piro (2019) decompTumor2Sig: Identification of mutational signatures active in individual tumors. BMC Bioinformatics 20(Suppl 4):152.

### See Also

`decompTumor2Sig`
`readShiraishiSignatures`

### Examples

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

[Package decompTumor2Sig version 2.10.0 Index]