Package 'VCFArray'

VCFArraySeed or VCFArray related methods, slot getters and setters.

Description

dim, dimnames: dimension and dimnames of object contained in the VCF file.

vcffile: extract the VcfFile object corresponding to the backend VCF file.

rowRanges: extract the rowRanges information from the backend VCF file.

Usage

## S4 method for signature 'VCFArraySeed'
dim(x)

## S4 method for signature 'VCFArraySeed'
dimnames(x)

vcffile(x)

## S4 method for signature 'VCFArraySeed'
vcffile(x)

## S4 method for signature 'VCFArraySeed'
rowRanges(x)

## S4 method for signature 'VCFArraySeed'
show(object)

## S4 method for signature 'VCFArray'
vcffile(x)

## S4 method for signature 'VCFArray'
rowRanges(x)

Arguments

x	the VCFArray or VCFArraySeed objects.
object	the VCFArraySeed object.

Value

dim: the integer vector of dimensions for VCFArray or VCFArraySeed objects.

dimnames: the unnamed list of dimension names for VCFArray and VCFArraySeed objects.

vcffile: the VcfFile object corresponding to the backend VCF file.

Examples

fl <- system.file("extdata", "chr22.vcf.gz",
                  package="VariantAnnotation")
va <- VCFArray(fl, name = "GT")
dim(va)
dimnames(va)
vcffile(va)
seed(va)
dim(seed(va))
DelayedArray::type(va)

---

VCFArray constructor and coercion methods.

Description

extract_array: the function to extract data from a VCF file, by taking VCFArraySeed as input. This function is required by the DelayedArray for the seed contract.

VCFArray: The function to convert data entries inside VCF file into the VCFArray instance.

Usage

## S4 method for signature 'VCFArraySeed'
extract_array(x, index)

VCFArray(file, vindex = character(), name = NA, pfix = NULL)

Arguments

x	the VCFArraySeed object
index	in extract_array(), an unnamed list of subscripts as positive integer vectors, one vector per dimension in x. Empty and missing subscripts (represented by integer(0) and NULL list elements, respectively) are allowed. The subscripts can contain duplicated indices. They cannot contain NAs or non-positive values.
file	takes values for charater string (specifying the VCF file path), VcfFile object, and RangedVcfStack object.
vindex	in VCFArray(), the character string specifying the index file path. This argument is required if an remote VCF file is used for the file argument.
name	the data entry from VCF file to be read into VCFArraySeed / VCFArray. For VCFArray. This argument should always be specified.
pfix	the category that the name belongs to. Available values are fixed, info, and info. Can also Check vcfFields(file) for matching name and pfix.

Value

VCFArray class object.

Examples

fl <- system.file("extdata", "chr22.vcf.gz",
                  package="VariantAnnotation")
va <- VCFArray(fl, name = "GT")
va
vcf <- VariantAnnotation::VcfFile(fl)
va1 <- VCFArray(vcf, name = "GT")
va1
all.equal(va, va1)
## Not run: 
## RangedVcfStack class
extdata <- system.file(package = "GenomicFiles", "extdata")
files <- dir(extdata, pattern="^CEUtrio.*bgz$", full=TRUE)[1:2]
names(files) <- sub(".*_([0-9XY]+).*", "\\1", basename(files))
seqinfo <- as(readRDS(file.path(extdata, "seqinfo.rds")), "Seqinfo")
stack <- GenomicFiles::VcfStack(files, seqinfo)
gr <- as(GenomicFiles::seqinfo(stack)[rownames(stack)], "GRanges")
## RangedVcfStack
rgstack <- GenomicFiles::RangedVcfStack(stack, rowRanges = gr)
rgstack
va2 <- VCFArray(rgstack, name = "SB")
va2

## End(Not run)
## coercion
as(va[1:10, ], "array")

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