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\name{ScanVcfParam-class}
\docType{class}
\alias{ScanVcfParam}
\alias{ScanVcfParam-class}
\alias{ScanVcfParam,missing-method}
\alias{ScanVcfParam,ANY-method}
\alias{vcfFixed}
\alias{vcfFixed<-}
\alias{vcfInfo}
\alias{vcfInfo<-}
\alias{vcfGeno}
\alias{vcfGeno<-}
\alias{vcfSamples}
\alias{vcfSamples<-}
\alias{vcfTrimEmpty}
\alias{vcfTrimEmpty<-}
\alias{vcfWhich}
\alias{vcfWhich<-}
\title{Parameters for scanning VCF files}
\description{
Use \code{ScanVcfParam()} to create a parameter object influencing
which records and fields are imported from a VCF file. Record
parsing is based on genomic coordinates and requires a Tabix index
file. Individual VCF elements can be specified in the \sQuote{fixed},
\sQuote{info}, \sQuote{geno} and \sQuote{samples} arguments.
}
\usage{
ScanVcfParam(fixed=character(), info=character(), geno=character(),
samples=character(), trimEmpty=TRUE, which, ...)
## Getters and Setters
vcfFixed(object)
vcfFixed(object) <- value
vcfInfo(object)
vcfInfo(object) <- value
vcfGeno(object)
vcfGeno(object) <- value
vcfSamples(object)
vcfSamples(object) <- value
vcfTrimEmpty(object)
vcfTrimEmpty(object) <- value
vcfWhich(object)
vcfWhich(object) <- value
}
\arguments{
\item{fixed}{A character() vector of fixed fields to be returned. Possible
values are ALT, QUAL and FILTER. The CHROM, POS, ID and REF fields are
needed to create the \code{GRanges} of variant locations. Because these
are essential fields there is no option to request or omit them. If not
specified, all fields are returned; if \code{fixed=NA} only REF is
returned.
}
\item{info}{A character() vector naming the \sQuote{INFO} fields to return.
\code{scanVcfHeader()} returns a vector of available fields. If not
specified, all fields are returned; if \code{info=NA} no fields are returned.
}
\item{geno}{A character() vector naming the \sQuote{GENO} fields to return.
\code{scanVcfHeader()} returns a vector of available fields. If not specified,
all fields are returned; if \code{geno=NA} no fields are returned and
requests for specific samples are ignored.
}
\item{samples}{A character() vector of sample names to return.
\code{samples(scanVcfHeader())} returns all possible names. If not
specified, data for all samples are returned; if either
\code{samples=NA} or \code{geno=NA} no fields are returned. Requests
for specific samples when \code{geno=NA} are ignored.
}
\item{trimEmpty}{A logical(1) indicating whether \sQuote{GENO} fields
with no values should be returned.
}
\item{which}{A \code{\linkS4class{GRanges}} or \code{\linkS4class{RangedData}}
describing the sequences and ranges to be queried. Variants whose \code{POS}
lies in the interval(s) \code{[start, end]} are returned. If \code{which} is
not specified all ranges are returned.
}
\item{object}{An instance of class \code{ScanVcfParam}.
}
\item{value}{An instance of the corresponding slot, to be assigned to
\code{object}.
}
\item{\dots}{Arguments passed to methods.
}
}
\section{Objects from the Class}{
Objects can be created by calls of the form \code{ScanVcfParam()}.
}
\section{Slots}{
\describe{
\item{\code{which}:}{Object of class \code{"RangesList"} indicating
which reference sequence and coordinate variants must overlap.
}
\item{\code{fixed}:}{Object of class \code{"character"} indicating
fixed fields to be returned.
}
\item{\code{info}:}{Object of class \code{"character"} indicating
portions of \sQuote{INFO} to be returned.
}
\item{\code{geno}:}{Object of class \code{"character"} indicating
portions of \sQuote{GENO} to be returned.
}
\item{\code{samples}:}{Object of class \code{"character"} indicating
the samples to be returned.
}
\item{\code{trimEmpty}:}{Object of class \code{"logical"} indicating
whether empty \sQuote{GENO} fields are to be returned.
}
}
}
\section{Functions and methods}{
See 'Usage' for details on invocation.
Constructor:
\describe{
\item{ScanVcfParam:}{Returns a \code{ScanVcfParam} object.
The \code{which} argument to the constructor can be one of several types,
as documented above.}
}
Accessors:
\describe{
\item{vcfFixed, vcfInfo, vcfGeno, vcfSamples, vcfTrimEmpty, vcfWhich:}{
Return the corresponding field from \code{object}.
}
}
Methods:
\describe{
\item{show}{Compactly display the object.
}
}
}
\author{
Martin Morgan and Valerie Obenchain <vobencha@fhcrc.org>
}
\seealso{
\code{\link{readVcf}}
}
\examples{
ScanVcfParam()
fl <- system.file("extdata", "structural.vcf", package="VariantAnnotation")
compressVcf <- bgzip(fl, tempfile())
idx <- indexTabix(compressVcf, "vcf")
tab <- TabixFile(compressVcf, idx)
## ---------------------------------------------------------------------
## 'which' argument
## ---------------------------------------------------------------------
## To subset on genomic coordinates, supply an object
## containing the ranges of interest. These ranges can
## be given directly to the 'param' argument or wrapped
## inside ScanVcfParam() as the 'which' argument.
## When using a list, the outer list names must correspond to valid
## chromosome names in the vcf file. In this example they are "1"
## and "2".
gr1 <- GRanges("1", IRanges(13219, 2827695, name="regionA"))
gr2 <- GRanges(rep("2", 2), IRanges(c(321680, 14477080),
c(321689, 14477090), name=c("regionB", "regionC")))
grl <- GRangesList("1"=gr1, "2"=gr2)
vcf <- readVcf(tab, "hg19", grl)
## Names of the individual ranges are returned in the
## 'paramRangeID' column in the rowData,
rowData(vcf)
## which can be used for subsetting the VCF object
vcf[rowData(vcf)$paramRangeID == "regionA"]
## When using ranges, the seqnames must correspond to valid
## chromosome names in the vcf file.
gr <- unlist(grl, use.names=FALSE)
vcf <- readVcf(tab, "hg19", gr)
## ---------------------------------------------------------------------
## 'fixed', 'info', 'geno' and 'samples' arguments
## ---------------------------------------------------------------------
## This param specifies the "GT" 'geno' field for a single sample
## and the subset of ranges in 'which'. All 'fixed' and 'info' fields
## will be returned.
ScanVcfParam(geno="GT", samples="NA00002", which=gr)
## Here two 'fixed' and one 'geno' field are specified
ScanVcfParam(fixed=c("ALT", "QUAL"), geno="GT", info=NA)
## Return only the 'fixed' fields
ScanVcfParam(geno=NA, info=NA)
}
\keyword{classes}
|
