buildSortedAlexandrovSignaturePatternList: buildSortedAlexandrovSignaturePatternList (internal function)

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

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
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.

decompTumor2Sig documentation built on Nov. 8, 2020, 8:23 p.m.