VCFHeader-class {VariantAnnotation} | R Documentation |
The VCFHeader
class holds Variant Call Format (VCF) file
header information and is produced from a call to scanVcfHeader
.
The VCFHeader
class is holds header information from a
from VCF file.
Slots :
reference
character() vector
sample
character() vector
header
DataFrameList-class
VCFHeader(reference = character(), samples = character(),
header = DataFrameList(), ...)
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
.
A character() vector of sequences.
A character() vector of sample names.
A DataFrameList
of parsed header lines
(preceeded by “##”) present in the VCF file.
Additional arguments passed to methods.
Valerie Obenchain
fl <- system.file("extdata", "structural.vcf", package="VariantAnnotation") hdr <- scanVcfHeader(fl) fixed(hdr) info(hdr) geno(hdr)