buildGenomesFromMutationData: buildGenomesFromMutationData (internal function)

View source: R/buildGenomesFromMutationData.R

buildGenomesFromMutationDataR Documentation

buildGenomesFromMutationData (internal function)

Description

Build genome data structures (same as signatures) and fill then with mutation data.

Usage

buildGenomesFromMutationData(snvs, numBases, type, trDir,
uniqueTrDir=TRUE, refGenome, transcriptAnno, verbose)

Arguments

snvs

SNV matrix (see description above).

numBases

Number of bases for the sequence pattern (odd integer).

type

Type of signature to be used ("Alexandrov", "Shiraishi").

trDir

Logical: use transcription-strand information?

uniqueTrDir

Logical; used only if trDir is also TRUE: if uniqueTrDir is TRUE (default), then only mutations with only one defined transcription strand will be used, mutations for which both strands are valid are ignored. If FALSE, these mutations are accepted and one of the two transcription strands will be arbitrarily taken (the first one encountered in the databse specified for transcriptAnno). The latter was the behavior until version 1.3.5 of decompTumor2Sig and is also the behavior of pmsignature.

refGenome

Reference genome (BSgenome object).

transcriptAnno

Transcription information (TxDb object).

verbose

Logical. Print additional information?

Details

SNVs are specified as a matrix of the following format (adapted from VCF):
#> snvs[1:2,]
# CHROM POS REF ALT FORMAT sample1 sample2
#[1,] "2" "947" "C" "T" "GT:PL:GQ:AD:DP" "1/1:84,6,0:6:0,2:2" NA
#[2,] "2" "992" "G" "A" "GT:PL:GQ:AD:DP" "0/1:123,0,33:33:1,3:4" "0/0:..."

Value

A list of genomes: each genome is represented by the observed frequencies of mutation patterns according to the selected signature type.

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.


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