VCFHeader instances

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

Constructor

VCFHeader: 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.

Details

The VCFHeader class holds header information from a VCF file.

Slots :

reference: character() vector
sample: character() vector
header: DataFrameList class

Author

Valerie Obenchain

Examples

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

  fixed(hdr)
#> DataFrameList of length 2
#> names(2): FILTER ALT
  info(hdr)
#> DataFrame with 10 rows and 3 columns
#>                Number        Type            Description
#>           <character> <character>            <character>
#> BKPTID              .      String ID of the assembled ..
#> CIEND               2     Integer Confidence interval ..
#> CIPOS               2     Integer Confidence interval ..
#> END                 1     Integer End position of the ..
#> HOMLEN              .     Integer Length of base pair ..
#> HOMSEQ              .      String Sequence of base pai..
#> IMPRECISE           0        Flag Imprecise structural..
#> MEINFO              4      String Mobile element info ..
#> SVLEN               .     Integer Difference in length..
#> SVTYPE              1      String Type of structural v..
  geno(hdr)
#> DataFrame with 4 rows and 3 columns
#>          Number        Type            Description
#>     <character> <character>            <character>
#> GT            1      String               Genotype
#> GQ            1       Float       Genotype quality
#> CN            1     Integer Copy number genotype..
#> CNQ           1       Float Copy number genotype..
  vcfFields(hdr)
#> CharacterList of length 4
#> [["fixed"]] REF ALT QUAL FILTER
#> [["info"]] BKPTID CIEND CIPOS END HOMLEN HOMSEQ IMPRECISE MEINFO SVLEN SVTYPE
#> [["geno"]] GT GQ CN CNQ
#> [["samples"]] NA00001