VcfFile {VariantAnnotation} | R Documentation

## Manipulate Variant Call Format (Vcf) files.

### Description

Use `VcfFile()` to create a reference to a Vcf file (and its index). Once opened, the reference remains open across calls to methods, avoiding costly index re-loading.

`VcfFileList()` provides a convenient way of managing a list of `VcfFile` instances.

### usage

## Constructors

  VcfFile(file, index = paste(file, "tbi", sep="."), ..., yieldSize=NA_integer_)

  VcfFileList(..., yieldSize=NA_integer_)

## Accessors

  index(object)

  path(object, ...)

  isOpen(con, rw="")

  yieldSize(object, ...)

  yieldSize(object, ...) <- value

  show(object)

## Opening / closing

  open(con, ...)

  close(con, ...)

## method

  vcfFields(object)

### arguments

- conAn instance of `VcfFile`.

- fileA character(1) vector to the Vcf file path; can be remote (http://, ftp://).

- indexA character(1) vector of the Vcf file index (.tbi file).

- yieldSizeNumber of records to yield each time the file is read from using `scanVcf` or `readVcf`.

- ...Additional arguments. For `VcfFileList`, this can either be a single character vector of paths to Vcf files, or several instances of `VcfFile` objects.

- rwcharacter() indicating mode of file.

### Objects from the Class

Objects are created by calls of the form `VcfFile()`.

### Fields

`VcfFile` and `VcfFileList` classes inherit fields from the `TabixFile` and `TabixFileList` classes.

### Functions and methods

`VcfFile` and `VcfFileList` classes inherit methods from the `TabixFile` and `TabixFileList` classes.

## Opening / closing:

open

  Opens the (local or remote) `path` and `index`. Returns a `VcfFile` instance. `yieldSize` determines the number of records parsed during each call to `scanVcf` or `readVcf`; `NA` indicates that all records are to be parsed.

close

  Closes the `VcfFile` `con`; returning (invisibly) the updated `VcfFile`. The instance may be re-opened with `open.VcfFile`.

## Accessors:

path

  Returns a character(1) vector of the Vcf path name.

index

  Returns a character(1) vector of Vcf index (tabix file) name.

yieldSize, yieldSize<-

  Return or set an integer(1) vector indicating yield size.

## Methods:

vcfFields

  Returns a `CharacterList` of all available VCF fields, with names of `fixed`, `info`, `geno` and `samples` indicating the four categories. Each element is a character() vector of available VCF field names within each category. It works for both local and remote vcf file.

### Author(s)

Valerie Obenchain

### Examples

    fl <- system.file("extdata", "chr7-sub.vcf.gz", package="VariantAnnotation",
                      mustWork=TRUE)
    vcffile <- VcfFile(fl)
    vcffile
    vcfFields(fl)
    vcfFields(vcffile)

    param <- GRanges("7", IRanges(c(55000000,  55900000), width=10000))
    vcf <- readVcf(vcffile, "hg19", param=param)
    dim(vcf)

    ## `vcfFields` also works for remote vcf filepath.
    ## Not run:
    chr22url <- "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz"
    vcfFields(chr22url)

    ## End(Not run)

[Package VariantAnnotation version 1.30.1 Index]