convertGenomesFromVRanges: Convert genomes from a 'VRanges' object

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

Description

'convertGenomesFromVRanges()' converts the SNVs of a single tumor genome (sample) or a set of genomes from a VRanges object (package VariantAnnotation) and determines the mutation frequencies according to a specific model of mutational signatures (Alexandrov or Shiraishi), such that the resulting format can be used as genomes input for decomposeTumorGenomes.

Usage

convertGenomesFromVRanges(vranges, numBases=5, type="Shiraishi",
trDir=TRUE, enforceUniqueTrDir=TRUE, 
refGenome=BSgenome.Hsapiens.UCSC.hg19::BSgenome.Hsapiens.UCSC.hg19,
transcriptAnno=
TxDb.Hsapiens.UCSC.hg19.knownGene::TxDb.Hsapiens.UCSC.hg19.knownGene,
verbose=TRUE)

Arguments

vranges	(Mandatory) The VRanges object which specifies the mutations.
numBases	(Mandatory) Total number of bases (mutated base and flanking bases) to be used for sequence patterns. Must be odd. Default: 5
type	(Mandatory) Signature model or type ("Alexandrov" or "Shiraishi"). Default: "Shiraishi"
trDir	(Mandatory) Specifies whether the transcription direction is taken into account in the signature model. If so, only mutations within genomic regions with a defined transcription direction can be considered. Default: TRUE
enforceUniqueTrDir	(Optional) Used only if trDir is TRUE. If enforceUniqueTrDir is TRUE (default), then mutations which map to a region with multiple overlapping genes with opposing transcription directions will be excluded from the analysis. If FALSE, the transcript direction encountered first in the transcript database (see transcriptAnno) is assigned to the mutation. The latter was the behavior until version 1.3.5 of decompTumor2Sig and is also the behavior of pmsignature. However, it is preferable to exclude these mutations from the count (default) because from mutation data alone it cannot be inferred which of the two genes has the higher transcriptional activity which might potentially be linked to the occurrence of the mutation. (If you are unsure, use the default setting; this option exists mostly for backward compatibility with older versions.)
refGenome	(Mandatory) The reference genome (BSgenome) needed to extract sequence patterns. Default: BSgenome object for hg19.
transcriptAnno	(Optional) Transcript annotation (TxDb object) used to determine the transcription direction. This is required only if trDir is TRUE. Default: TxDb object for hg19.
verbose	(Optional) Print information about reading and processing the mutation data. Default: TRUE

Value

A list containing the genomes in terms of frequencies of the mutated sequence patterns. This list of genomes can be used for decomposeTumorGenomes.

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.

See Also

decompTumor2Sig
decomposeTumorGenomes
readGenomesFromVCF
readGenomesFromMPF
getGenomesFromMutFeatData

Examples

### load the reference genome and the transcript annotation database
refGenome <- BSgenome.Hsapiens.UCSC.hg19::BSgenome.Hsapiens.UCSC.hg19
transcriptAnno <-
  TxDb.Hsapiens.UCSC.hg19.knownGene::TxDb.Hsapiens.UCSC.hg19.knownGene

### take the breast cancer genomes from Nik-Zainal et al (PMID: 22608084) 
gfile <- system.file("extdata",
         "Nik-Zainal_PMID_22608084-VCF-convertedfromMPF.vcf.gz", 
         package="decompTumor2Sig")

### get the corresponding VRanges object (using the VariantAnnotation
### package)
library(VariantAnnotation)
vr <- readVcfAsVRanges(gfile, genome="hg19")

### convert the VRanges object to the decompTumor2Sig format
genomes <- convertGenomesFromVRanges(vr, numBases=5, type="Shiraishi",
         trDir=TRUE, enforceUniqueTrDir=TRUE, refGenome=refGenome, 
         transcriptAnno=transcriptAnno, verbose=FALSE)

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