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 holds header information from a 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`. Each `DataFrame` represents a unique "key" name in the header file. Multiple header lines with the same "key" are parsed into the same `DataFrame` with the "ID" field as the row names. Simple header lines have no "ID" field in which case the "key" is used as the row name.

  NOTE: In VariantAnnotation <= 1.27.25, the `meta()` extractor returned a `DataFrame` called "META" which held all simple key-value header lines. The VCF 4.3 specs allowed headers lines with key name "META" which caused a name clash with the pre-existing "META" `DataFrame`.

  In `VariantAnnotation` >=1.27.26 the "META" `DataFrame` was split and each row became its own separate `DataFrame`. Calling `meta()` on a `VCFHeader` object now returns a list of `DataFrames`, one for each unique key name in the header.

  `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`.

  `vcfFields(x)`: 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.

### 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)
      vcfFields(hdr)

[Package VariantAnnotation version 1.30.1 Index]