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\name{refLocsToLocalLocs}
\alias{refLocsToLocalLocs}
\alias{refLocsToLocalLocs,GRanges,TranscriptDb,missing-method}
\alias{refLocsToLocalLocs,GRanges,missing,GRangesList-method}
\title{refLocsToLocalLocs}
\description{
Converts reference locations (aka chromosome-based or genomic)
to coding regions, and protein based locations
}
\usage{
refLocsToLocalLocs(ranges, txdb, cdsbytx, ...)
\S4method{refLocsToLocalLocs}{GRanges,TranscriptDb,missing}(ranges, txdb, cdsbytx, ...)
\S4method{refLocsToLocalLocs}{GRanges,missing,GRangesList}(ranges, txdb, cdsbytx, ...)
}
\arguments{
\item{ranges}{A \link[GenomicRanges]{GRanges} object containing
the variants in reference-based coordinates.
}
\item{txdb}{A \link[GenomicFeatures]{TranscriptDb} object that serves
as the annotation reference.
}
\item{cdsbytx}{A \link[GenomicRanges]{GRangesList} object with transcripts
as the outer list elements and coding regions as the inner.
}
\item{\dots}{Additional arguments passed to methods
}
}
\details{
This function translates the reference-based coordinates in \code{ranges} to
\sQuote{local} coordinates in the coding region (CDS) and protein sequences.
When a \code{txdb} is suplied the \code{cdsbytx} is created with
\code{cdsBy()}. If \code{cdsbytx} is provided the outer list elements must be
transcripts and the inner list elements represent coding regions. The
\code{GRangesList} objects must have names on the outer list
elements (i.e., transcript names).
Only ranges that fall \sQuote{within} coding sequences are reported in the
result. Output is a modified \code{GRanges} of the \code{ranges} input where
each row represents a range-transcript match making multiple rows per range
posible. The \code{elementMetadata} columns include \code{tx_id},
\code{cdsLoc} and \code{proteinLoc}. When a \code{txdb} is provided the
\code{txId} is the internal transcript id from the annotation. When
\code{cdsbytx} is provided \code{tx_id} are the names on the outer list
elements.
If \code{ranges} is unstranded the strand of the return value reflects the
strand of the subject the \code{ranges} overlapped with.
}
\value{
A \link[GenomicRanges]{GRanges} with the following \code{elementMetadata}
columns,
\describe{
\item{\code{CDSLOC}}{
Location in coding region coordinates
}
\item{\code{PROTEINLOC}}{
Location in protein (codon triplet) coordinates
}
\item{\code{QUERYID}}{
Character vector mapping to the of rows of the original \code{query}
}
\item{\code{TXID}}{
Character vector of internal transcript ids from the
\link[GenomicFeatures]{TranscriptDb} or the names of the outer list
elements of the \code{cdsbytx} object.
}
\item{\code{CDSID}}{
Character vector of internal coding region ids from the
\link[GenomicFeatures]{TranscriptDb} or the names of the outer list
elements of the \code{cdsbytx} object.
}
}
}
\author{Michael Lawrence and Valerie Obenchain <vobencha@fhcrc.org>}
\seealso{
\link[IRanges]{map}
\code{predictCoding}
\code{getTranscriptSeqs}
\link[GenomicFeatures]{transcriptLocs2refLocs}
\link[GenomicFeatures]{extractTranscriptSeqs}
}
\examples{
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
ranges <- GRanges(c("chr12", "chr1", "chr5"),
IRanges(c(1017956, 881906, 140532),
c(1017956, 881907, 140532)))
refLocsToLocalLocs(ranges, TxDb.Hsapiens.UCSC.hg19.knownGene)
}
\keyword{manip}
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