VCFArray-classes: VCFArray constructor and coercion methods.
In VCFArray: Representing on-disk / remote VCF files as array-like objects

Description Usage Arguments Value Examples

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.

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

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

`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`.

VCFArray class object.

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")