buildGenomesFromMutationData {decompTumor2Sig} | R 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
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]