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\name{VCFHeader-class}
\docType{class}
% Class
\alias{VCFHeader-class}
% Constructor-like function:
\alias{VCFHeader}
% Accessor methods:
\alias{reference}
\alias{reference,VCFHeader-method}
\alias{samples}
\alias{samples,VCFHeader-method}
\alias{header}
\alias{header,VCFHeader-method}
\alias{contig}
\alias{contig,VCFHeader-method}
\alias{meta}
\alias{meta,VCFHeader-method}
\alias{meta<-}
\alias{meta<-,VCFHeader,DataFrame-method}
\alias{fixed,VCFHeader-method}
\alias{fixed<-,VCFHeader,DataFrameList-method}
\alias{info,VCFHeader-method}
\alias{info<-,VCFHeader,DataFrame-method}
\alias{geno,VCFHeader-method}
\alias{geno<-,VCFHeader,missing,DataFrame-method}
% show method:
\alias{show,VCFHeader-method}
\title{VCFHeader instances}
\description{
The \code{VCFHeader} class holds Variant Call Format (VCF) file
header information and is produced from a call to \code{scanVcfHeader}.
}
\section{Constructor}{
\describe{
\item{}{
\code{VCFHeader(reference = character(), samples = character(),
header = DataFrameList(), ...)
}
}
}
}
\section{Accessors}{
In the following code snippets \code{x} is a VCFHeader object.
\describe{
\item{}{
\code{samples(x)}:
Returns a character() vector of names of samples.
}
\item{}{
\code{header(x)}:
Returns all information in the header slot which includes
\code{meta}, \code{info} and \code{geno} if present.
}
\item{}{
\code{meta(x)}, \code{meta(x)<- value}:
Gets or sets a \code{DataFrame} of meta information. This includes
any information represented as simple key-value pairs in the
VCF file header. Replacement value must be a \code{DataFrame}
with a single column named \sQuote{Value}.
}
\item{}{
\code{fixed(x), fixed(x)<- value}:
Returns a \code{DataFrameList} of information pertaining to any of
\sQuote{REF}, \sQuote{ALT}, \sQuote{FILTER} and \sQuote{QUAL}.
Replacement value must be a \code{DataFrameList} with names
\sQuote{QUAL} or \sQuote{FILTER}.
}
\item{}{
\code{info(x)}, \code{info(x)<- value}:
Gets or sets a \code{DataFrame} of \sQuote{INFO} information.
Replacement value must be a \code{DataFrame} with 3 columns
named \sQuote{Number}, \sQuote{Type} and \sQuote{Description}.
}
\item{}{
\code{geno(x)}, \code{geno(x)<- value}:
Returns a \code{DataFrame} of \sQuote{FORMAT} information.
Replacement value must be a \code{DataFrame} with 3 columns
named \sQuote{Number}, \sQuote{Type} and \sQuote{Description}.
}
\item{}{
\code{reference(x)}:
Returns a character() vector with names of reference sequences.
Not relevant for \code{scanVcfHeader}.
}
}
}
\section{Arguments}{
\describe{
\item{reference}{A character() vector of sequences.
}
\item{sample}{A character() vector of sample names.
}
\item{header}{A \code{DataFrameList} of parsed header lines
(preceeded by \dQuote{##}) present in the VCF file.
}
\item{...}{Additional arguments passed to methods.
}
}
}
\details{
The \code{VCFHeader} class is holds header information from a
from VCF file.
Slots :
\describe{
\item{\code{reference}}{character() vector
}
\item{\code{sample}}{character() vector
}
\item{\code{header}}{\link{DataFrameList}-class
}
}
}
\author{Valerie Obenchain <vobencha@fhcrc.org>}
\seealso{
\code{\link{scanVcfHeader}},
\link[IRanges]{DataFrameList}
}
\examples{
fl <- system.file("extdata", "structural.vcf", package="VariantAnnotation")
hdr <- scanVcfHeader(fl)
fixed(hdr)
info(hdr)
geno(hdr)
}
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