VCFHeader-class: VCFHeader instances
In Bioconductor/VariantAnnotation: Annotation of Genetic Variants

VCFHeader-class

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 <= 1.27.5, 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 >=1.27.6 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

Examples

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

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

Bioconductor/VariantAnnotation documentation built on Nov. 2, 2024, 7:22 a.m.