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Viewing changes to man/findSpliceOverlaps-methods.Rd

  • Committer: Package Import Robot
  • Author(s): Andreas Tille
  • Date: 2013-11-26 19:52:13 UTC
  • mfrom: (1.1.1)
  • Revision ID: package-import@ubuntu.com-20131126195213-1zwbthnie0a7fdns
Tags: 1.14.3-1
http://bugs.debian.org/730574
* New upstream version
  Closes: #730574
* Build-Depends: r-bioc-xvector

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man/findSpliceOverlaps-methods.Rd
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\alias{findSpliceOverlaps}
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\alias{findSpliceOverlaps-methods}
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\alias{findSpliceOverlaps,GappedAlignments,GRangesList-method}
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\alias{findSpliceOverlaps,GappedAlignmentPairs,GRangesList-method}
 
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\alias{findSpliceOverlaps,GAlignments,GRangesList-method}
 
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\alias{findSpliceOverlaps,GAlignmentPairs,GRangesList-method}
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\alias{findSpliceOverlaps,GRangesList,GRangesList-method}
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\title{Classify ranges (reads) as compatible with existing genomic annotations 
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\usage{
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findSpliceOverlaps(query, subject, ignore.strand=FALSE, ...)
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\S4method{findSpliceOverlaps}{GappedAlignments,GRangesList}(query, subject, ignore.strand=FALSE, ..., cds=NULL)
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\S4method{findSpliceOverlaps}{GappedAlignmentPairs,GRangesList}(query, subject, ignore.strand=FALSE, ..., cds=NULL)
 
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\S4method{findSpliceOverlaps}{GAlignments,GRangesList}(query, subject, ignore.strand=FALSE, ..., cds=NULL)
 
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\S4method{findSpliceOverlaps}{GAlignmentPairs,GRangesList}(query, subject, ignore.strand=FALSE, ..., cds=NULL)
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\S4method{findSpliceOverlaps}{GRangesList,GRangesList}(query, subject, ignore.strand=FALSE, ..., cds=NULL)
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## Low-level utils:
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\arguments{
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  \item{query}{
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    \code{character} name of a Bam file, a \link[Rsamtools]{BamFile}, 
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    \linkS4class{GappedAlignments}, \linkS4class{GappedAlignmentPairs} 
 
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    \linkS4class{GAlignments}, \linkS4class{GAlignmentPairs} 
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    or a \linkS4class{GRangesList} object containing the reads.
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    Single or paired-end reads are specified with the \code{singleEnd} 
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    argument (default FALSE). Paired-end reads can be supplied in a Bam 
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    file or \linkS4class{GappedAlignmentPairs} object. Single-end are
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    expected to be in a Bam file, \linkS4class{GappedAlignments} or 
 
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    file or \linkS4class{GAlignmentPairs} object. Single-end are
 
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    expected to be in a Bam file, \linkS4class{GAlignments} or 
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    \linkS4class{GRanges} object.
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  }
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  \item{subject}{
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    in a coding region. When not provided, the "coding" output is 
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    \code{NA}.
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  }
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  \item{\dots}{
 
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  \item{...}{
 
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    Additional arguments such as \code{singleEnd} used in the BamFile method. 
 
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    \describe{
 
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      \item{singleEnd}{
 
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        A logical value indicating if reads are single or paired-end.
 
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      }
 
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    }
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  }
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}
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\seealso{
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  \itemize{
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    \item The \link{GRangesList}, \link{GappedAlignments}, and
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          \link{GappedAlignmentPairs} classes.
 
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    \item The \link{GRangesList}, \link{GAlignments}, and
 
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          \link{GAlignmentPairs} classes.
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  }
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}
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hits2 <- findSpliceOverlaps(pe, exbytx, singleEnd=FALSE, param=param)
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## In addition to Bam files, paired-end reads can be supplied in a 
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## GappedAlignmentPairs object. 
 
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## GAlignmentPairs object. 
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genes <- GRangesList(
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    GRanges("chr1", IRanges(c(5, 20), c(10, 25)), "+"),
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    GRanges("chr1", IRanges(c(5, 22), c(15, 25)), "+"))
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galp <- GappedAlignmentPairs(
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    GappedAlignments("chr1", 5L, "11M4N6M", strand("+")),
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    GappedAlignments("chr1", 50L, "6M", strand("-")),
 
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galp <- GAlignmentPairs(
 
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    GAlignments("chr1", 5L, "11M4N6M", strand("+")),
 
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    GAlignments("chr1", 50L, "6M", strand("-")),
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    isProperPair=TRUE)
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findSpliceOverlaps(galp, genes)
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}