1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
|
\name{map-methods}
\alias{map,GenomicRanges,GAlignments-method}
\title{Mapping ranges between sequences}
\description{
A method for translating a set of input ranges through a
\link{GAlignments} object. Returns a \linkS4class{RangesMapping}
object.
NOTE: The \code{\link[IRanges]{map}} generic function is defined and
documented in the \pkg{IRanges} package.
A method for translating a set of input ranges through a
\link[GenomicRanges]{GRangesList} object is defined and documented
in the \pkg{GenomicRanges} package.
}
\usage{
\S4method{map}{GenomicRanges,GAlignments}(from, to)
}
\arguments{
\item{from}{The input ranges to map, usually
a \code{\linkS4class{GenomicRanges}}}
\item{to}{The alignment between the sequences in \code{from} and the
sequences in the result.}
}
\value{
An object of class \code{RangesMapping}. The \pkg{GenomicRanges}
package provides some additional methods on this object.
See \code{?`\link[GenomicRanges]{map-methods}`} in the \pkg{GenomicRanges}
package for more information.
}
\details{
Each element in \code{to} is taken to represent the
alignment of a (read) sequence. The CIGAR string is used to
translate the input ranges to be relative to the read start. This
is useful, for example, when determining the cycle (read position)
at which a particular genomic mismatch occurs.
}
\seealso{
The \linkS4class{RangesMapping} class is the typical return value.
}
\author{M. Lawrence}
|
