SeqVarGDSClass {SeqArray} | R Documentation

## SeqVarGDSClass

### Description

A `SeqVarGDSClass` object provides access to a GDS file containing Variant Call Format (VCF) data. It extends `gds.class`.

### Details

A SeqArray GDS file is created from a VCF file with `seqVCF2GDS`. This file can be opened with `seqOpen` to create a `SeqVarGDSClass` object.

### Accessors

In the following code snippets `x` is a SeqVarGDSClass object.

  `granges(x)`: Returns the chromosome and position of variants as a `GRanges` object. Names correspond to the variant.id.

  `ref(x)`: Returns the reference alleles as a `DNAStringSet`.

  `alt(x)`: Returns the alternate alleles as a `DNAStringSetList`.

  `qual(x)`: Returns the quality scores.

  `filt(x)`: Returns the filter data.

  `fixed(x)`: Returns the fixed fields (ref, alt, qual, filt).

  `header(x)`: Returns the header as a `DataFrameList`.

  `rowRanges(x)`: Returns a `GRanges` object with metadata.

  `colData(x)`: Returns a `DataFrame` with sample identifiers and any information in the 'sample.annotation' node.

  `info(x, info=NULL)`: Returns the info fields as a `DataFrame`. `info` is a character vector with the names of fields to return (default is to return all).

  `geno(x, geno=NULL)`: Returns the geno (format) fields as a `SimpleList`. `geno` is a character vector with the names of fields to return (default is to return all).

Other data can be accessed with `seqGetData`.

### Coercion methods

In the following code snippets `x` is a SeqVarGDSClass object.

  `seqAsVCF(x, chr.prefix="", info=NULL, geno=NULL)`:

### Author(s)

Stephanie Gogarten, Xiuwen Zheng

### See Also

`gds.class`, `seqOpen`

### Examples

    gds <- seqOpen(seqExampleFileName("gds"))
    gds

    ## sample ID
    head(seqGetData(gds, "sample.id"))

    ## variants
    granges(gds)

    ## Not run:
    ## alleles as comma-separated character strings
    head(seqGetData(gds, "allele"))

    ## alleles as DNAStringSet or DNAStringSetList
    ref(gds)
    v <- alt(gds)

    ## genotype
    geno <- seqGetData(gds, "genotype")
    dim(geno)
    ## dimensions are: allele, sample, variant
    geno[1,1:10,1:5]

    ## rsID
    head(seqGetData(gds, "annotation/id"))

    ## alternate allele count
    head(seqGetData(gds, "annotation/info/AC"))

    ## individual read depth
    depth <- seqGetData(gds, "annotation/format/DP")
    names(depth)
    ## VCF header defined DP as variable-length data
    table(depth$length)
    ## all length 1, so depth$data should be a sample by variant matrix
    dim(depth$data)
    depth$data[1:10,1:5]

    ## End(Not run)

    seqClose(gds)

[Package SeqArray version 1.26.2 Index]