VCFHeader-class {VariantAnnotation} | R Documentation

## VCFHeader instances

### Description

The `VCFHeader` class holds Variant Call Format (VCF) file header information and is produced from a call to `scanVcfHeader`.

### Details

The `VCFHeader` class is holds header information from a from VCF file.

Slots :

`reference`

  character() vector

`sample`

  character() vector

`header`

  DataFrameList-class

### Constructor

  `VCFHeader(reference = character(), samples = character(), header = DataFrameList(), ...)`

### Accessors

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

  `samples(x)`: Returns a character() vector of names of samples.

  `header(x)`: Returns all information in the header slot which includes `meta`, `info` and `geno` if present.

  `meta(x)`, `meta(x)<- value`: The getter returns a `DataFrameList` with possible names of META, SAMPLE and PEDIGREE. The META `DataFrame` is a catch-all for non-standard header fields. This includes any information represented as simple key-value pairs. The replacement `value` can be a `DataFrame` or `DataFrameList`.

  `fixed(x), fixed(x)<- value`: Returns a `DataFrameList` of information pertaining to any of ‘REF’, ‘ALT’, ‘FILTER’ and ‘QUAL’. Replacement value must be a `DataFrameList` with one or more of the following names, ‘QUAL’, ‘FILTER’, ‘REF’ and ‘ALT’.

  `info(x)`, `info(x)<- value`: Gets or sets a `DataFrame` of ‘INFO’ information. Replacement value must be a `DataFrame` with 3 columns named ‘Number’, ‘Type’ and ‘Description’.

  `geno(x)`, `geno(x)<- value`: Returns a `DataFrame` of ‘FORMAT’ information. Replacement value must be a `DataFrame` with 3 columns named ‘Number’, ‘Type’ and ‘Description’.

  `reference(x)`: Returns a character() vector with names of reference sequences. Not relevant for `scanVcfHeader`.

### Arguments

reference

  A character() vector of sequences.

sample

  A character() vector of sample names.

header

  A `DataFrameList` of parsed header lines (preceeded by “##”) present in the VCF file.

...

  Additional arguments passed to methods.

### Author(s)

Valerie Obenchain

### See Also

`scanVcfHeader`, `DataFrameList`

### Examples

      fl <- system.file("extdata", "structural.vcf", package="VariantAnnotation")
      hdr <- scanVcfHeader(fl)

      fixed(hdr)
      info(hdr)
      geno(hdr)

[Package VariantAnnotation version 1.24.5 Index]