VariantAnnotation (version 1.18.1)

VCF-class: VCF class objects

Description

The VCF class is a virtual class extended from RangedSummarizedExperiment. The subclasses, CompressedVCF and ExtendedVCF, are containers for holding data from Variant Call Format files.

genotypeCodesToNucleotides(vcf, ...)

This function converts the `GT` genotype codes in a VCF object to nucleotides. See also ?readGT to read in only `GT` data as codes or nucleotides.

SnpMatrixToVCF(from, seqSource)

This function converts the output from the read.plink function to a VCF class. from must be a list of length 3 with named elements "map", "fam" and "genotypes". seqSource can be a BSgenome or an FaFile used for reference sequence extraction.

Variant Type

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

Details

The VCF class is a virtual class with two concrete subclasses, CollapsedVCF and ExtendedVCF.

Slots unique to VCF and subclasses,

• fixed: ADataFramecontaining the REF, ALT, QUAL and FILTER fields from a VCF file.
• info: ADataFramecontaining the INFO fields from a VCF file.

Slots inherited from RangedSummarizedExperiment,

• metadata: Alistcontaining the file header or other information about the overall experiment.
• rowRanges: AGRanges-class instance defining the variant ranges and associated metadata columns of REF, ALT, QUAL and FILTER.
• colData: ADataFrame-class instance describing the samples and associated metadata.
• geno: Theassaysslot fromRangedSummarizedExperimenthas been renamed asgenofor the VCF class. This slot contains the genotype information immediately following the FORMAT field in a VCF file. Each element of thelistorSimpleListis a matrix or array.

It is expected that users will not create instances of the VCF class but instead one of the concrete subclasses, CollapsedVCF or ExpandVCF. CollapsedVCF contains the ALT data as a DNAStringSetList allowing for multiple alleles per variant. The ExpandedVCF ALT data is a DNAStringSet where the ALT column has been expanded to create a flat form of the data with one row per variant-allele combination. In the case of strucutral variants, ALT will be a CompressedCharacterList or character in the collapsed or expanded forms.

See Also

GRanges, DataFrame, SimpleList, RangedSummarizedExperiment, readVcf, writeVcf isSNV

Examples

fl <- system.file("extdata", "structural.vcf", package="VariantAnnotation")
vcf <- readVcf(fl, genome="hg19")

## ----------------------------------------------------------------
## Accessors 
## ----------------------------------------------------------------
## Variant locations are stored in the GRanges object returned by
## the rowRanges() accessor.
rowRanges(vcf)

## Individual fields can be extracted with ref(), alt(), qual() 
## and filt().
qual(vcf)
ref(vcf)

## All 'info' fields can be extracted together along
## with the GRanges of locations.
head(info(vcf))

## All genotype fields can be seen with geno(). Individual
## fields are accessed with '$' or '[['.
geno(vcf)
identical(geno(vcf)$GQ, geno(vcf)[[2]])

## ----------------------------------------------------------------
## Renaming seqlevels and subsetting 
## ----------------------------------------------------------------
## Overlap and matching operations require that the objects
## being compared have the same seqlevels (chromosome names).
## It is often the case that the seqlevesls in on of the objects
## needs to be modified to match the other. In this VCF, the 
## seqlevels are numbers instead of preceded by "chr" or "ch". 

seqlevels(vcf)

## Rename the seqlevels to start with 'chr'.
vcf2 <- renameSeqlevels(vcf, paste0("chr", seqlevels(vcf))) 
seqlevels(vcf2)

## The VCF can also be subset by seqlevel using 'keepSeqlevels'
## or 'dropSeqlevels'. See ?keepSeqlevels for details. 
vcf3 <- keepSeqlevels(vcf2, "chr2")
seqlevels(vcf3)

## ----------------------------------------------------------------
## Header information 
## ----------------------------------------------------------------

## Header data can be modified in the 'meta', 'info' and 'geno'
## slots of the VCFHeader object. See ?VCFHeader for details.

## Current 'info' fields.
rownames(info(header(vcf)))

## Add a new field to the header.
newInfo <- DataFrame(Number=1, Type="Integer",
                     Description="Number of Samples With Data",
                     row.names="NS")
info(header(vcf)) <- rbind(info(header(vcf)), newInfo)
rownames(info(header(vcf)))

## ----------------------------------------------------------------
## Collapsed and Expanded VCF 
## ----------------------------------------------------------------
## readVCF() produces a CollapsedVCF object.
fl <- system.file("extdata", "ex2.vcf", 
                  package="VariantAnnotation")
vcf <- readVcf(fl, genome="hg19")
vcf

## The ALT column is a DNAStringSetList to allow for more
## than one alternate allele per variant.
alt(vcf)

## For structural variants ALT is a CharacterList.
fl <- system.file("extdata", "structural.vcf", 
                  package="VariantAnnotation")
vcf <- readVcf(fl, genome="hg19")
alt(vcf)

## ExpandedVCF is the 'flattened' counterpart of CollapsedVCF.
## The ALT and all variables with Number='A' in the header are
## expanded to one row per alternate allele.
vcfLong <- expand(vcf)
alt(vcfLong)

## Also see the ?VRanges class for an alternative form of
## 'flattened' VCF data.

## ----------------------------------------------------------------
## isSNV()
## ----------------------------------------------------------------
## isSNV() returns a subset VCF containing SNVs only.

vcf <- VCF(rowRanges = GRanges("chr1", IRanges(1:4*3, width=c(1, 2, 1, 1))))
alt(vcf) <- DNAStringSetList("A", c("TT"), c("G", "A"), c("TT", "C"))
ref(vcf) <- DNAStringSet(c("G", c("AA"), "T", "G"))
fixed(vcf)[c("REF", "ALT")]

## SNVs are present in rows 1 (single ALT value), 3 (both ALT values) 
## and 4 (1 of the 2 ALT values).
vcf[isSNV(vcf, singleAltOnly=TRUE)] 
vcf[isSNV(vcf, singleAltOnly=FALSE)] ## all 3 SNVs