extract_array {VCFArray} | R Documentation |
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)
x |
the VCFArraySeed object |
index |
in |
file |
takes values for charater string (specifying the VCF
file path), |
vindex |
in |
name |
the data entry from VCF file to be read into
VCFArraySeed / VCFArray. For |
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")