VCFArray-methods: VCFArraySeed or VCFArray related methods, slot getters and...

In Bioconductor/VCFArray: Representing on-disk / remote VCF files as array-like objects

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)

Bioconductor/VCFArray documentation built on Oct. 26, 2023, 6:38 a.m.