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, ...)

### 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.

### Author(s)

Valerie Obenchain

### Examples

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

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

[Package VariantAnnotation version 1.26.1 Index]