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]