buildSortedAlexandrovSignaturePatternList {decompTumor2Sig} | R Documentation

## buildSortedAlexandrovSignaturePatternList (internal function)

### Description

Build and sort the pattern list of an Alexandrov signature in the following way: First according to the base change: C>A, C>G, C>T, T>A, T>C, T>G, then within these categories according to the flanking bases: A, C, G, T.

### Usage

    buildSortedAlexandrovSignaturePatternList(numBases, trDir)

### Arguments

`numBases` | Number of bases for the sequence pattern (odd integer).
`trDir` | Logical: use transcription-strand information?

### Value

A sorted list of mutation features (e.g., triplets with base change).

### 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.

[Package decompTumor2Sig version 2.0.0 Index]