readAlexandrovSignatures: Read Alexandrov-type signatures (COSMIC format).

In rmpiro/decompTumor2Sig: Decomposition of individual tumors into mutational signatures by signature refitting

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: <[e-mail]> or <[e-mail]>

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()

rmpiro/decompTumor2Sig documentation built on May 15, 2022, 3:27 a.m.