\name{GappedAlignments-class} \docType{class} % Class: \alias{class:GappedAlignments} \alias{GappedAlignments-class} % Constructors: \alias{GappedAlignments} \alias{updateObject,GappedAlignments-method} \alias{readGappedAlignments} % Accessors: \alias{length,GappedAlignments-method} \alias{names,GappedAlignments-method} \alias{seqnames,GappedAlignments-method} \alias{rname} \alias{rname,GappedAlignments-method} \alias{strand,GappedAlignments-method} \alias{names<-,GappedAlignments-method} \alias{seqnames<-,GappedAlignments-method} \alias{rname<-} \alias{rname<-,GappedAlignments-method} \alias{strand<-,GappedAlignments-method} \alias{cigar} \alias{cigar,GappedAlignments-method} \alias{qwidth} \alias{qwidth,GappedAlignments-method} \alias{start,GappedAlignments-method} \alias{end,GappedAlignments-method} \alias{width,GappedAlignments-method} \alias{ngap,GappedAlignments-method} \alias{elementMetadata,GappedAlignments-method} \alias{elementMetadata<-,GappedAlignments-method} \alias{seqinfo,GappedAlignments-method} \alias{seqinfo<-,GappedAlignments-method} % Coercion: \alias{grglist} \alias{granges} \alias{rglist} \alias{grglist,GappedAlignments-method} \alias{granges,GappedAlignments-method} \alias{rglist,GappedAlignments-method} \alias{ranges,GappedAlignments-method} \alias{coerce,GappedAlignments,GRangesList-method} \alias{coerce,GappedAlignments,GRanges-method} \alias{coerce,GappedAlignments,RangesList-method} \alias{coerce,GappedAlignments,Ranges-method} \alias{as.data.frame,GappedAlignments-method} % Subsetting: \alias{[,GappedAlignments-method} % Combining: \alias{c,GappedAlignments-method} % "show" method: \alias{show,GappedAlignments-method} % Other methods: \alias{qnarrow} \alias{qnarrow,GappedAlignments-method} \alias{narrow,GappedAlignments-method} % Old stuff (deprecated or defunct): \alias{grg} \title{GappedAlignments objects} \description{ The GappedAlignments class is a simple container which purpose is to store a set of alignments that will hold just enough information for supporting the operations described below. } \details{ A GappedAlignments object is a vector-like object where each element describes an alignment i.e. how a given sequence (called "query" or "read", typically short) aligns to a reference sequence (typically long). Typically, a GappedAlignments object will be created by loading records from a BAM (or SAM) file and each element in the resulting object will correspond to a record. BAM/SAM records generally contain a lot of information but only part of that information is loaded in the GappedAlignments object. In particular, we discard the query sequences (SEQ field), the query qualities (QUAL), the mapping qualities (MAPQ) and any other information that is not needed in order to support the operations or methods described below. This means that multi-reads (i.e. reads with multiple hits in the reference) won't receive any special treatment i.e. the various SAM/BAM records corresponding to a multi-read will show up in the GappedAlignments object as if they were coming from different/unrelated queries. Also paired-end reads will be treated as single-end reads and the pairing information will be lost (see \code{?\link{GappedAlignmentPairs}} for how to handle aligned paired-end reads). Each element of a GappedAlignments object consists of: \itemize{ \item The name of the reference sequence. (This is the RNAME field in a SAM/BAM record.) \item The strand in the reference sequence to which the query is aligned. (This information is stored in the FLAG field in a SAM/BAM record.) \item The CIGAR string in the "Extended CIGAR format" (see the SAM Format Specifications for the details). \item The 1-based leftmost position/coordinate of the clipped query relative to the reference sequence. We will refer to it as the "start" of the query. (This is the POS field in a SAM/BAM record.) \item The 1-based rightmost position/coordinate of the clipped query relative to the reference sequence. We will refer to it as the "end" of the query. (This is NOT explicitly stored in a SAM/BAM record but can be inferred from the POS and CIGAR fields.) Note that all positions/coordinates are always relative to the first base at the 5' end of the plus strand of the reference sequence, even when the query is aligned to the minus strand. \item The genomic intervals between the "start" and "end" of the query that are "covered" by the alignment. Saying that the full [start,end] interval is covered is the same as saying that the alignment has no gap (no N in the CIGAR). It is then considered a simple alignment. Note that a simple alignment can have mismatches or deletions (in the reference). In other words, a deletion, encoded with a D, is NOT considered a gap. } Note that the last 2 items are not expicitly stored in the GappedAlignments object: they are inferred on-the-fly from the CIGAR and the "start". Optionally, a GappedAlignments object can have names (accessed thru the \code{\link[base]{names}} generic function) which will be coming from the QNAME field of the SAM/BAM records. The rest of this man page will focus on describing how to: \itemize{ \item Access the information stored in a GappedAlignments object in a way that is independent from how the data are actually stored internally. \item How to create and manipulate a GappedAlignments object. } } \section{Constructors}{ \describe{ \item{}{ \code{readGappedAlignments(file, format="BAM", use.names=FALSE, ...)}: Read a file containing aligned reads as a GappedAlignments object. By default (i.e. \code{use.names=FALSE}), the resulting object has no names. If \code{use.names} is \code{TRUE}, then the names are constructed from the query template names (QNAME field in a SAM/BAM file). Note that this function is just a front-end that delegates to the format-specific back-end function specified via the \code{format} argument. The \code{use.names} argument and any extra argument are passed to the back-end function. Only the BAM format is supported for now. Its back-end is the \code{\link[Rsamtools]{readBamGappedAlignments}} function defined in the Rsamtools package. See \code{?\link[Rsamtools]{readBamGappedAlignments}} for more information (you might need to install and load the Rsamtools package first). } \item{}{ \code{GappedAlignments(seqnames=Rle(factor()), pos=integer(0), cigar=character(0), strand=NULL, names=NULL, seqlengths=NULL, ...)}: Low-level GappedAlignments constructor. Generally not used directly. Named arguments in \code{...} are used as elementMetadata. } } } \section{Accessors}{ In the code snippets below, \code{x} is a GappedAlignments object. \describe{ \item{}{ \code{length(x)}: Returns the number of alignments in \code{x}. } \item{}{ \code{names(x)}, \code{names(x) <- value}: Gets or sets the names of \code{x}. See \code{readGappedAlignments} above for how to automatically extract and set the names from the file to read. } \item{}{ \code{seqnames(x)}, \code{seqnames(x) <- value}: Gets or sets the name of the reference sequence for each alignment in \code{x} (see Details section above for more information about the RNAME field of a SAM/BAM file). \code{value} can be a factor, or a 'factor' \link[IRanges]{Rle}, or a character vector. } \item{}{ \code{rname(x)}, \code{rname(x) <- value}: Same as \code{seqnames(x)} and \code{seqnames(x) <- value}. } \item{}{ \code{strand(x)}, \code{strand(x) <- value}: Gets or sets the strand for each alignment in \code{x} (see Details section above for more information about the strand of an alignment). \code{value} can be a factor (with levels +, - and *), or a 'factor' \link[IRanges]{Rle}, or a character vector. } \item{}{ \code{cigar(x)}: Returns a character vector of length \code{length(x)} containing the CIGAR string for each alignment. } \item{}{ \code{qwidth(x)}: Returns an integer vector of length \code{length(x)} containing the length of the query *after* hard clipping (i.e. the length of the query sequence that is stored in the corresponding SAM/BAM record). } \item{}{ \code{start(x)}, \code{end(x)}: Returns an integer vector of length \code{length(x)} containing the "start" and "end" (respectively) of the query for each alignment. See Details section above for the exact definitions of the "start" and "end" of a query. Note that \code{start(x)} and \code{end(x)} are equivalent to \code{start(granges(x))} and \code{end(granges(x))}, respectively (or, alternatively, to \code{min(rglist(x))} and \code{max(rglist(x))}, respectively). } \item{}{ \code{width(x)}: Equivalent to \code{width(granges(x))} (or, alternatively, to \code{end(x) - start(x) + 1L}). Note that this is generally different from \code{qwidth(x)} except for alignments with a trivial CIGAR string (i.e. a string of the form \code{"M"} where is a number). } \item{}{ \code{ngap(x)}: Returns an integer vector of length \code{length(x)} containing the number of gaps for each alignment. Equivalent to \code{elementLengths(rglist(x)) - 1L}. } \item{}{ \code{seqinfo(x)}, \code{seqinfo(x) <- value}: Gets or sets the information about the underlying sequences. \code{value} must be a \link{Seqinfo} object. } \item{}{ \code{seqlevels(x)}, \code{seqlevels(x) <- value}: Gets or sets the sequence levels. \code{seqlevels(x)} is equivalent to \code{seqlevels(seqinfo(x))} or to \code{levels(seqnames(x))}, those 2 expressions being guaranteed to return identical character vectors on a GappedAlignments object. \code{value} must be a character vector with no NAs. See \code{?\link{seqlevels}} for more information. } \item{}{ \code{seqlengths(x)}, \code{seqlengths(x) <- value}: Gets or sets the sequence lengths. \code{seqlengths(x)} is equivalent to \code{seqlengths(seqinfo(x))}. \code{value} can be a named non-negative integer or numeric vector eventually with NAs. } \item{}{ \code{isCircular(x)}, \code{isCircular(x) <- value}: Gets or sets the circularity flags. \code{isCircular(x)} is equivalent to \code{isCircular(seqinfo(x))}. \code{value} must be a named logical vector eventually with NAs. } \item{}{ \code{genome(x)}, \code{genome(x) <- value}: Gets or sets the genome identifier or assembly name for each sequence. \code{genome(x)} is equivalent to \code{genome(seqinfo(x))}. \code{value} must be a named character vector eventually with NAs. } } } \section{Coercion}{ In the code snippets below, \code{x} is a GappedAlignments object. \describe{ \item{}{ \code{grglist(x, order.as.in.query=FALSE, drop.D.ranges=FALSE)}, \code{rglist(x, order.as.in.query=FALSE, drop.D.ranges=FALSE)}: Returns either a \link{GRangesList} or a \link[IRanges]{RangesList} object of length \code{length(x)} where the i-th element represents the ranges (with respect to the reference) of the i-th alignment in \code{x}. More precisely, the \link[IRanges]{RangesList} object returned by \code{rglist(x)} is a \link[IRanges]{CompressedIRangesList} object. The \code{order.as.in.query} toggle affects the order of the ranges \emph{within} each top-level element of the returned object. If \code{FALSE} (the default), then the ranges are ordered from 5' to 3' in elements associated with the plus strand (i.e. corresponding to alignments located on the plus strand), and from 3' to 5' in elements associated with the minus strand. So, whatever the strand is, the ranges are in ascending order (i.e. left-to-right). If \code{TRUE}, then the order of the ranges in elements associated with the \emph{minus} strand is reversed. So they end up being ordered from 5' to 3' too, which means that they are now in decending order (i.e. right-to-left). It also means that, when \code{order.as.in.query=TRUE} is used, the ranges are \emph{always} ordered consistently with the original "query template", that is, in the order defined by walking the "query template" from the beginning to the end. If \code{drop.D.ranges} is \code{TRUE}, then deletions (Ds in the CIGAR) are treated like gaps (Ns in the CIGAR), that is, the ranges corresponding to deletions are dropped. See Details section above for more information. } \item{}{ \code{granges(x)}, \code{ranges(x)}: Returns either a \link{GRanges} or a \link[IRanges]{Ranges} object of length \code{length(x)} where each element represents the regions in the reference to which a query is aligned. More precisely, the \link[IRanges]{Ranges} object returned by \code{ranges(x)} is an \link[IRanges]{IRanges} object. } \item{}{ \code{as(x, "GRangesList")}, \code{as(x, "GRanges")}, \code{as(x, "RangesList")}, \code{as(x, "Ranges")}: An alternate way of doing \code{grglist(x)}, \code{granges(x)}, \code{rglist(x)}, \code{ranges(x)}, respectively. } } } \section{Subsetting and related operations}{ In the code snippets below, \code{x} is a GappedAlignments object. \describe{ \item{}{ \code{x[i]}: Returns a new GappedAlignments object made of the selected alignments. \code{i} can be a numeric or logical vector. } } } \section{Combining}{ \describe{ \item{}{ \code{c(...)}: Concatenates the GappedAlignment objects in \code{...}. } } } \section{Other methods}{ \describe{ \item{}{ \code{qnarrow(x, start=NA, end=NA, width=NA)}: \code{x} is a GappedAlignments object. Returns a new GappedAlignments object of the same length as \code{x} describing how the narrowed query sequences align to the reference. The \code{start}/\code{end}/\code{width} arguments describe how to narrow the query sequences. They must be vectors of integers. NAs and negative values are accepted and "solved" according to the rules of the SEW (Start/End/Width) interface (see \code{?\link[IRanges]{solveUserSEW}} for the details). } \item{}{ \code{narrow(x, start=NA, end=NA, width=NA)}: \code{x} is a GappedAlignments object. Returns a new GappedAlignments object of the same length as \code{x} describing the narrowed alignments. Unlike with \code{qnarrow} now the \code{start}/\code{end}/\code{width} arguments describe the narrowing on the reference side, not the query side. Like with \code{qnarrow}, they must be vectors of integers. NAs and negative values are accepted and "solved" according to the rules of the SEW (Start/End/Width) interface (see \code{?\link[IRanges]{solveUserSEW}} for the details). } } } \references{ \url{http://samtools.sourceforge.net/} } \author{ H. Pages and P. Aboyoun } \seealso{ \itemize{ \item \link{GappedAlignmentPairs-class}. \item \code{\link[Rsamtools]{readBamGappedAlignments}}. \item \link{GRangesList-class}. \item \link{GRanges-class}. \item \link{findOverlaps-methods}. \item \link{coverage-methods}. \item \code{\link{seqinfo}}. \item \link[IRanges]{CompressedIRangesList-class}. \item \link{setops-methods}. } } \examples{ library(Rsamtools) # for ScanBamParam() and the ex1.bam file ex1_file <- system.file("extdata", "ex1.bam", package="Rsamtools") gal <- readGappedAlignments(ex1_file, param=ScanBamParam(what="flag")) gal ## --------------------------------------------------------------------- ## A. BASIC MANIPULATION ## --------------------------------------------------------------------- length(gal) head(gal) names(gal) # no names by default seqnames(gal) seqlevels(gal) ## Rename the reference sequences: seqlevels(gal) <- sub("seq", "chr", seqlevels(gal)) seqlevels(gal) strand(gal) head(cigar(gal)) head(qwidth(gal)) table(qwidth(gal)) grglist(gal) # a GRangesList object granges(gal) # a GRanges object rglist(gal) # a CompressedIRangesList object ranges(gal) # an IRanges object stopifnot(identical(elementLengths(grglist(gal)), elementLengths(rglist(gal)))) head(start(gal)) head(end(gal)) head(width(gal)) head(ngap(gal)) ## --------------------------------------------------------------------- ## B. SUBSETTING ## --------------------------------------------------------------------- gal[strand(gal) == "-"] gal[grep("I", cigar(gal), fixed=TRUE)] gal[grep("N", cigar(gal), fixed=TRUE)] # no gaps ## A confirmation that all the queries map to the reference with no ## gaps: stopifnot(all(ngap(gal) == 0)) ## Different ways to subset: gal[6] # a GappedAlignments object of length 1 grglist(gal)[[6]] # a GRanges object of length 1 rglist(gal)[[6]] # a NormalIRanges object of length 1 ## Ds are NOT gaps: ii <- grep("D", cigar(gal), fixed=TRUE) gal[ii] ngap(gal[ii]) grglist(gal[ii]) ## qwidth() vs width(): gal[qwidth(gal) != width(gal)] ## This MUST return an empty object: gal[cigar(gal) == "35M" & qwidth(gal) != 35] ## but this doesn't have too: gal[cigar(gal) != "35M" & qwidth(gal) == 35] ## --------------------------------------------------------------------- ## C. qnarrow()/narrow() ## --------------------------------------------------------------------- ## Note that there is no difference between qnarrow() and narrow() when ## all the alignments are simple and with no indels. ## This trims 3 nucleotides on the left and 5 nucleotides on the right ## of each alignment: qnarrow(gal, start=4, end=-6) ## Note that the 'start' and 'end' arguments specify what part of each ## query sequence should be kept (negative values being relative to the ## right end of the query sequence), not what part should be trimmed. ## Trimming on the left doesn't change the "end" of the queries. qnarrow(gal, start=21) stopifnot(identical(end(qnarrow(gal, start=21)), end(gal))) } \keyword{methods} \keyword{classes}