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\alias{coerce,GAlignmentsList,GRanges-method}
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\alias{coerce,GAlignmentsList,RangesList-method}
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\alias{coerce,GAlignmentsList,Ranges-method}
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\alias{coerce,GAlignmentPairs,GAlignmentsList-method}
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\alias{grglist,GAlignmentsList-method}
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\alias{granges,GAlignmentsList-method}
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\alias{rglist,GAlignmentsList-method}
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\alias{ranges,GAlignmentsList-method}
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\alias{introns,GAlignmentsList-method}
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\alias{[,GAlignmentsList-method}
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\alias{[<-,GAlignmentsList,ANY,ANY,ANY-method}
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\alias{[[<-,GAlignmentsList-method}
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\alias{[[<-,GAlignmentsList,ANY,ANY-method}
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\alias{c,GAlignmentsList-method}
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The GAlignmentsList class is a container for storing a collection of
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GappedAlignments objects.
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\link{GAlignments} objects.
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A GAlignmentsList object contains a list of GappedAlignments. The
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majority of operations on this page are described in more detail
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on the GappedAlignments man page, see ?\code{GappedAlignments}.
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A GAlignmentsList object contains a list of \link{GAlignments} objects.
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The majority of operations on this page are described in more detail
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on the GAlignments man page, see ?\code{GAlignments}.
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\section{Constructors}{
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\code{GAlignmentsList(...)}:
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Creates a GAlignmentsList from a list of GappedAlignments objects.
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Creates a GAlignmentsList from a list of \link{GAlignments} objects.
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\code{readGAlignmentsList(file, format="BAM", use.names=FALSE, ...)}:
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Read a file containing aligned reads as a GAlignmentsList object.
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Note that this function is just a front-end that delegates to the
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\code{\link[Rsamtools]{readBamGAlignmentsList}} function defined
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\code{\link[Rsamtools]{readGAlignmentsListFromBam}} function defined
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in the Rsamtools package.
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See \code{?\link[Rsamtools]{readBamGAlignmentsList}} for
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See \code{?\link[Rsamtools]{readGAlignmentsListFromBam}} for
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The \code{param} and \code{asProperPairs} arguments described on the
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\code{\link[Rsamtools]{readBamGAlignmentsList}} man page fine tune the
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records are returned. \code{param} is specifed by the standard
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\code{ScanBamParam()} options. When \code{asProperPairs=TRUE} (default),
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only the proper pairs are returned. This is the same QC filtering that
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is done by \code{readBamGappedAlignmentPairs} but the records are
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returned in a \code{GAlignmentsList} instead of
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\code{GappedAlignmentsPairs} object. If \code{asProperPairs=FALSE}, all
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records in the file are retained (i.e., no QC) and the list structure is
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split by read id (QNAME in SAM/BAM). This format allows the flexibility
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to retain singletons, pairs, and multi-fragment reads in a single class.
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The \code{param} described on the
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\code{\link[Rsamtools]{readGAlignmentsListFromBam}} man page fine tunes
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which records are returned and how they are grouped. \code{param} is
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specified by the standard \code{ScanBamParam()} options.
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the cigar information. The resulting ranges span the entire
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range, including any gaps or spaces between paired-end reads.
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The \code{granges} coercion supports \code{ignore.strand} to
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allow ranges of opposite strand to be combined (see examples).
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\code{granges} coercion supports \code{ignore.strand} to allow
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ranges of opposite strand to be combined (see examples). All
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ranges in the resulting GRanges will have strand \sQuote{*}.
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\code{grglist(x, ignore.strand=FALSE)},
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\code{rglist(x)}:
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Return either a \link{GRangesList} or a \link[IRanges]{IRangesList}
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object of length \code{length(x)}. This coercion RESPECTS the cigar
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information. The resulting ranges are fragments of the original ranges
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that do not include gaps or spaces between paired-end reads.
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that do not include gaps or spaces between paired-end reads.
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\code{grglist} coercion supports \code{ignore.strand} to allow
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ranges of opposite strand to be combined (see examples). All
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ranges in the resulting GRangesList will have strand \sQuote{*}.
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\code{as(x, "GRangesList")}, \code{as(x, "GRanges")},
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\item \link{GappedAlignments-class}.
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\item \link{GappedAlignmentPairs-class}.
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\item \code{\link[Rsamtools]{readBamGappedAlignments}}.
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\item \code{\link[Rsamtools]{readBamGappedAlignmentPairs}}.
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\item \link{GAlignments-class}.
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\item \link{GAlignmentPairs-class}.
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\item \code{\link[Rsamtools]{readGAlignmentsFromBam}}.
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\item \code{\link[Rsamtools]{readGAlignmentPairsFromBam}}.
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\item \link{findOverlaps-methods}.
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gal1 <- GappedAlignments(
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seqnames=Rle(factor(c("chr1", "chr2", "chr1", "chr3")),
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pos=1:10, cigar=paste0(10:1, "M"),
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strand=Rle(strand(c("-", "+", "*", "+", "-")), c(1, 2, 2, 3, 2)),
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names=head(letters, 10), score=1:10)
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gal2 <- GappedAlignments(
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seqnames=Rle(factor(c("chr2", "chr4")), c(3, 4)), pos=1:7,
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cigar=c("5M", "3M2N3M2N3M", "5M", "10M", "5M1N4M", "8M2N1M", "5M"),
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strand=Rle(strand(c("-", "+")), c(4, 3)),
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## C. mcols()/elementMetadata()
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## ---------------------------------------------------------------------
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## Metadata can be defined on the individual GappedAlignment elements
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## Metadata can be defined on the individual GAlignment elements
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## and the overall GAlignmentsList object. By default, 'level=between'
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## extracts the GALignmentsList metadata. Using 'level=within'
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## will extract the metadata on the individual GappedAliginments.
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## will extract the metadata on the individual GAlignments objects.
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mcols(galist) ## no metadata on the GAlignmentsList object
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mcols(galist, level="within")
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## ---------------------------------------------------------------------
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## D. readBamGAlignmentsList()
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## D. readGAlignmentsListFromBam()
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## ---------------------------------------------------------------------
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library(pasillaBamSubset)
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fl <- sortBam(untreated3_chr4(), tempfile(), byQname=TRUE)
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bf <- BamFile(fl, index=character(0), yieldSize=50, obeyQname=TRUE)
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galist <- readGAlignmentsList(bf, asProperPairs=FALSE)
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## 'file' as character.
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fl <- untreated3_chr4()
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galist1 <- readGAlignmentsList(fl)
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table(elementLengths(galist1))
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## When 'file' is a BamFile, 'asMates' must be TRUE. If FALSE,
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## the data are treated as single-end and each list element of the
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## GAlignmentsList will be of length 1. For single-end data
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## use readGAlignments() instead of readGAlignmentsList().
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bf <- BamFile(fl, yieldSize=3, asMates=TRUE)
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readGAlignmentsList(bf)
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## Use a 'param' to fine tune the results.
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param <- ScanBamParam(flag=scanBamFlag(isProperPair=TRUE))
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galist2 <- readGAlignmentsList(fl, param=param)
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## ---------------------------------------------------------------------
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## ---------------------------------------------------------------------
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## The granges() coercion supports 'ignore.strand' to allow ranges
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## from different strand to be combined. In this example paired-end
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## reads aligned to opposite strands were read into a GAlignmentsList.
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## If the desired operation is to combine these ranges, reguardless of
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## gaps or the space between pairs, 'ignore.strand' must be TRUE.
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## The granges() and grlist() coercions support 'ignore.strand' to
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## allow ranges from different strand to be combined. In this example
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## paired-end reads aligned to opposite strands were read into a
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## GAlignmentsList. If the desired operation is to combine these ranges,
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## reguardless of gaps or the space between pairs, 'ignore.strand' must be TRUE.
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granges(galist[1], ignore.strand=TRUE)
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granges(galist[1], ignore.strand=FALSE)
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## grglist() splits ranges by gap and the space bein each list element
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## grglist() splits ranges by gap and the space between list elements.
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galist <- GAlignmentsList(noGaps=gal1, Gaps=gal2)
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grglist(galist, ignore.strand=TRUE)
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\keyword{methods}
added
removed
man/GAlignmentsList-class.Rd
