buildGenomesFromMutationData: buildGenomesFromMutationData (internal function)

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

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: <[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.