VariantAnnotation (version 1.18.1)

VRanges-class: VRanges objects

Description

The VRanges class is a container for variant calls, including SNVs and indels. It extends GRanges to provide special semantics on top of a simple vector of genomic locations. While it is not as expressive as the VCF object, it is a simpler alternative that may be convenient for variant calling/filtering and similar exercises.

Variant Type

Functions to identify variant type include isSNV, isInsertion, isDeletion, isIndel, isSubstitution and isTransition. See the ?isSNV man page for details.

Details

VRanges extends GRanges to store the following components. Except where noted, the components are considered columns in the dataset, i.e., their lengths match the number of variants. Many columns can be stored as either an atomic vector or an Rle. [object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object] Except in the special circumstances described here, a VRanges may be treated like a GRanges. The range should span the sequence in ref. Indels are typically represented by the VCF convention, i.e., the start position is one upstream of the event. The strand is always constrained to be positive (+).

Indels, by convention, should be encoded VCF-style, with the upstream reference base prepended to the indel sequence. The ref/alt for a deletion of GCGT before A might be AGCGT/A and for an insertion might be A/AGCGT. Since the range always matches the ref sequence, this means a deletion will be the width of the deletion + 1, and an insertion is always of width 1.

VRanges and the VCF class: The VRanges and VCF classes encode different types of information and are semantically incompatible. While methods exist for converting a VCF object to a VRanges and vice versa, information is lost in the transformation. There is no way to collapse multiple rows of a VRanges at the same genomic position and accurately represent missing data. For this reason, it is not reasonable to assume that an object resulting from multiple conversions (VRanges -> VCF -> VRanges) will be equivalent to the original.

See Also

VRangesList, a list of VRanges; bam_tally in the gmapR package, which generates a VRanges.

Examples

## construction
vr <- VRanges(seqnames = c("chr1", "chr2"),
              ranges = IRanges(c(1, 10), c(5, 20)),
              ref = c("T", "A"), alt = c("C", "T"),
              refDepth = c(5, 10), altDepth = c(7, 6),
              totalDepth = c(12, 17), sampleNames = letters[1:2],
              hardFilters =
                FilterRules(list(coverage = function(x) totalDepth > 10)),
              softFilterMatrix =
                FilterMatrix(matrix = cbind(depth = c(TRUE, FALSE)),
                             FilterRules(depth = function(x) altDepth(x) > 6)),
              tumorSpecific = c(FALSE, TRUE))

## simple accessors
ref(vr)
alt(vr)
altDepth(vr)
vr$tumorSpecific
called(vr)

## coerce to VCF and write
vcf <- as(vr, "VCF")
## writeVcf(vcf, "example.vcf")
## or just
## writeVcf(vr, "example.vcf")

## other utilities
match(vr, vr[2:1])