Nothing
### -------------------------
### VCFArraySeed methods
### -------------------------
#' VCFArraySeed or VCFArray related methods, slot getters and setters.
#' @description \code{dim}, \code{dimnames}: dimension and dimnames of
#' object contained in the VCF file.
#' @param x the \code{VCFArray} or \code{VCFArraySeed} objects.
#' @return \code{dim}: the integer vector of dimensions for
#' \code{VCFArray} or \code{VCFArraySeed} objects.
#' @rdname VCFArray-methods
#' @exportMethod dim
#' @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)
setMethod("dim", "VCFArraySeed", function(x) x@dim)
#' @rdname VCFArray-methods
#' @export
#' @return \code{dimnames}: the unnamed list of dimension names for
#' \code{VCFArray} and \code{VCFArraySeed} objects.
setMethod("dimnames", "VCFArraySeed", function(x) x@dimnames)
#' @rdname VCFArray-methods
#' @export
setGeneric("vcffile", function(x) standardGeneric("vcffile"))
#' @description \code{vcffile}: extract the \code{VcfFile} object
#' corresponding to the backend VCF file.
#' @aliases vcffile vcffile,VCFArraySeed vcffile,VCFArray
#' @return \code{vcffile}: the \code{VcfFile} object corresponding to
#' the backend VCF file.
#' @rdname VCFArray-methods
setMethod("vcffile", "VCFArraySeed", function(x) x@vcffile)
#' @description \code{rowRanges}: extract the \code{rowRanges}
#' information from the backend VCF file.
#' @rdname VCFArray-methods
#' @export
setMethod("rowRanges", "VCFArraySeed", function(x) x@gr)
#' @export
#' @import VariantAnnotation
#' @import GenomicFiles
#' @importFrom Rsamtools index index<-
#' @param object the \code{VCFArraySeed} object.
#' @rdname VCFArray-methods
setMethod("show", "VCFArraySeed", function(object)
{
vcf <- vcffile(object)
if (is(vcf, "VcfFile")) {
cat("VCFArraySeed\n",
"VCF file path: ", path(vcf), "\n",
"VCF index path: ", index(vcf), "\n",
"array data: ", object@name, "\n",
"dim: ", paste(dim(object), collapse=" x "), "\n",
sep="")
} else if (is(vcf, "VcfStack")) {
vcffiles <- files(vcf)
cat("VCFArraySeed\n",
"VcfStack object with ", nrow(vcf), " files and ",
ncol(vcf), " samples", "\n",
"VCF file path: ",
"'", path(vcffiles[[1]]), "' and ",
nrow(vcf)-1, " more...", "\n",
"VCF index path: ",
"'", index(vcffiles[[1]]), "' and ",
nrow(vcf)-1, " more...", "\n",
"array data: ", object@name, "\n",
"dim: ", paste(dim(object), collapse=" x "), "\n",
sep="")
}
})
### -------------------
### VCFArray methods
### -------------------
#' @export
#' @rdname VCFArray-methods
setMethod("vcffile", "VCFArray", function(x) vcffile(seed(x)))
#' @export
#' @rdname VCFArray-methods
setMethod("rowRanges", "VCFArray", function(x) seed(x)@gr)
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