# GAlignmentPairs-class

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##### GAlignmentPairs objects

The GAlignmentPairs class is a container for "genomic alignment pairs".

Keywords
classes, methods
##### Details

A GAlignmentPairs object is a list-like object where each element describes a pair of genomic alignment.

An "alignment pair" is made of a "first" and a "last" alignment, and is formally represented by a GAlignments object of length 2. It is typically representing a hit of a paired-end read to the reference genome that was used by the aligner. More precisely, in a given pair, the "first" alignment represents the hit of the first end of the read (aka "first segment in the template", using SAM Spec terminology), and the "last" alignment represents the hit of the second end of the read (aka "last segment in the template", using SAM Spec terminology).

In general, a GAlignmentPairs object will be created by loading records from a BAM (or SAM) file containing aligned paired-end reads, using the readGAlignmentPairs function (see below). Each element in the returned object will be obtained by pairing 2 records.

##### Constructor

GAlignmentPairs(first, last, isProperPair, names=NULL): Low-level GAlignmentPairs constructor. Generally not used directly.

##### Accessors

In the code snippets below, x is a GAlignmentPairs object.

length(x): Return the number of alignment pairs in x.
names(x), names(x) <- value: Get or set the names on x. See readGAlignmentPairs for how to automatically extract and set the names when reading the alignments from a file.
first(x, invert.strand=FALSE), last(x, invert.strand=FALSE): Get the "first" or "last" alignment for each alignment pair in x. The result is a GAlignments object of the same length as x. If invert.strand=TRUE, then the strand is inverted on-the-fly, i.e. "+" becomes "-", "-" becomes "+", and "*" remains unchanged.
left(x): Get the "left" alignment for each alignment pair in x. By definition, the "left" alignment in a pair is the alignment that is on the + strand. If this is the "first" alignment, then it's returned as-is by left(x), but if this is the "last" alignment, then it's returned by left(x) with the strand inverted.
right(x): Get the "right" alignment for each alignment pair in x. By definition, the "right" alignment in a pair is the alignment that is on the - strand. If this is the "first" alignment, then it's returned as-is by right(x), but if this is the "last" alignment, then it's returned by right(x) with the strand inverted.
seqnames(x): Get the name of the reference sequence for each alignment pair in x. When reading the alignments from a BAM file, this comes from the RNAME field which has the same value for the 2 records in a pair (makeGAlignmentPairs, the function used by readGAlignmentPairsFromBam for doing the pairing, rejects pairs with incompatible RNAME values).
strand(x), strand(x) <- value: Get or set the strand for each alignment pair in x. By definition (and in a somewhat arbitrary way) the strand of an alignment pair is the strand of the "first" alignment in the pair. In a GAlignmentPairs object, the strand of the "last" alignment in a pair is typically (but not always) the opposite of the strand of the "first" alignment. Note that, currently, readGAlignmentPairsFromBam, the function used internally by readGAlignmentPairs for doing the pairing, rejects pairs where the "first" and "last" alignments are on the same strand, but those pairs might be supported in the future.
njunc(x): Equivalent to njunc(first(x)) + njunc(last(x)).
isProperPair(x): Get the "isProperPair" flag bit (bit 0x2 in SAM Spec) set by the aligner for each alignment pair in x.
seqinfo(x), seqinfo(x) <- value: Get or set the information about the underlying sequences. value must be a Seqinfo object.
seqlevels(x), seqlevels(x) <- value: Get or set the sequence levels. seqlevels(x) is equivalent to seqlevels(seqinfo(x)) or to levels(seqnames(x)), those 2 expressions being guaranteed to return identical character vectors on a GAlignmentPairs object. value must be a character vector with no NAs. See ?seqlevels for more information.
seqlengths(x), seqlengths(x) <- value: Get or set the sequence lengths. seqlengths(x) is equivalent to seqlengths(seqinfo(x)). value can be a named non-negative integer or numeric vector eventually with NAs.
isCircular(x), isCircular(x) <- value: Get or set the circularity flags. isCircular(x) is equivalent to isCircular(seqinfo(x)). value must be a named logical vector eventually with NAs.
genome(x), genome(x) <- value: Get or set the genome identifier or assembly name for each sequence. genome(x) is equivalent to genome(seqinfo(x)). value must be a named character vector eventually with NAs.
seqnameStyle(x): Get or set the seqname style for x. Note that this information is not stored in x but inferred by looking up seqnames(x) against a seqname style database stored in the seqnames.db metadata package (required). seqnameStyle(x) is equivalent to seqnameStyle(seqinfo(x)) and can return more than 1 seqname style (with a warning) in case the style cannot be determined unambiguously.

##### Vector methods

In the code snippets below, x is a GAlignmentPairs object.

x[i]: Return a new GAlignmentPairs object made of the selected alignment pairs.

##### List methods

In the code snippets below, x is a GAlignmentPairs object.

x[[i]]: Extract the i-th alignment pair as a GAlignments object of length 2. As expected x[[i]][1] and x[[i]][2] are respectively the "first" and "last" alignments in the pair.
unlist(x, use.names=TRUE): Return the GAlignments object conceptually defined by c(x[[1]], x[[2]], ..., x[[length(x)]]). use.names determines whether x names should be propagated to the result or not.

##### Coercion

In the code snippets below, x is a GAlignmentPairs object.

grglist(x, use.mcols=FALSE, order.as.in.query=FALSE, drop.D.ranges=FALSE): Return a GRangesList object of length length(x) where the i-th element represents the ranges (with respect to the reference) of the i-th alignment pair in x. If use.mcols is TRUE and x has metadata columns on it (accessible with mcols(x)), they're propagated to the returned object. IMPORTANT: The strand of the ranges coming from the "last" alignment in the pair is always inverted. The order.as.in.query toggle affects the order of the ranges within each top-level element of the returned object. If FALSE (the default), then the "left" ranges are placed before the "right" ranges, and, within each left or right group, are ordered from 5' to 3' in elements associated with the plus strand and from 3' to 5' in elements associated with the minus strand. More formally, the i-th element in the returned GRangesList object can be defined as c(grl1[[i]], grl2[[i]]), where grl1 is grglist(left(x)) and grl2 is grglist(right(x)). If TRUE, then the "first" ranges are placed before the "last" ranges, and, within each first or last group, are always ordered from 5' to 3', whatever the strand is. More formally, the i-th element in the returned GRangesList object can be defined as c(grl1[[i]], grl2[[i]]), where grl1 is grglist(first(x), order.as.in.query=TRUE) and grl2 is grglist(last(x, invert.strand=TRUE), order.as.in.query=TRUE). Note that the relationship between the 2 GRangesList objects obtained with order.as.in.query being respectively FALSE or TRUE is simpler than it sounds: the only difference is that the order of the ranges in elements associated with the minus strand is reversed. Finally note that, in the latter, the ranges are 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 drop.D.ranges is TRUE, then deletions (Ds in the CIGAR) are treated like junctions (Ns in the CIGAR), that is, the ranges corresponding to deletions are dropped.
granges(x, use.mcols=FALSE): Return a GRanges object of length length(x) where each range is obtained by merging all the ranges within the corresponding top-level element in grglist(x). If use.mcols is TRUE and x has metadata columns on it (accessible with mcols(x)), they're propagated to the returned object.
as(x, "GRangesList"), as(x, "GRanges"): Alternate ways of doing grglist(x, use.mcols=TRUE) and granges(x, use.mcols=TRUE), respectively.
as(x, "GAlignments"): Equivalent of unlist(x, use.names=TRUE).

##### Other methods

In the code snippets below, x is a GAlignmentPairs object.

show(x): By default the show method displays 5 head and 5 tail elements. This can be changed by setting the global options showHeadLines and showTailLines. If the object length is less than (or equal to) the sum of these 2 options plus 1, then the full object is displayed. Note that these options also affect the display of GRanges and GAlignments objects, as well as other objects defined in the IRanges and Biostrings packages (e.g. Ranges and XStringSet objects).

• readGAlignmentPairs for reading aligned paired-end reads from a file (typically a BAM file) into a GAlignmentPairs object.

• GAlignments objects for handling aligned single-end reads.

• makeGAlignmentPairs for pairing the elements of a GAlignments object into a GAlignmentPairs object.

• junctions-methods for extracting and summarizing junctions from a GAlignmentPairs object.

• coverage-methods for computing the coverage of a GAlignmentPairs object.

• findOverlaps-methods for finding range overlaps between a GAlignmentPairs object and another range-based object.

• seqinfo in the GenomeInfoDb package for getting/setting/modifying the sequence information stored in an object.

• The GRanges and GRangesList classes defined and documented in the GenomicRanges package.

##### Aliases
• class:GAlignmentPairs
• GAlignmentPairs-class
• GAlignmentPairs
• length,GAlignmentPairs-method
• names,GAlignmentPairs-method
• names<-,GAlignmentPairs-method
• first
• first,GAlignmentPairs-method
• last
• last,GAlignmentPairs-method
• left
• left,GAlignmentPairs-method
• right
• right,GAlignmentPairs-method
• seqnames,GAlignmentPairs-method
• strand,GAlignmentPairs-method
• strand<-,GAlignmentPairs-method
• njunc,GAlignmentPairs-method
• isProperPair
• isProperPair,GAlignmentPairs-method
• seqinfo,GAlignmentPairs-method
• seqlevelsInUse,GAlignmentPairs-method
• seqinfo<-,GAlignmentPairs-method
• [[,GAlignmentPairs,ANY,ANY-method
• unlist,GAlignmentPairs-method
• grglist,GAlignmentPairs-method
• granges,GAlignmentPairs-method
• coerce,GAlignmentPairs,GRangesList-method
• coerce,GAlignmentPairs,GRanges-method
• coerce,GAlignmentPairs,GAlignments-method
• show,GAlignmentPairs-method
• c,GAlignmentPairs-method
• ngap,GAlignmentPairs-method
##### Examples
library(Rsamtools)  # for the ex1.bam file
ex1_file <- system.file("extdata", "ex1.bam", package="Rsamtools")
galp

length(galp)
first(galp)
last(galp)
last(galp, invert.strand=TRUE)
left(galp)
right(galp)
seqnames(galp)
strand(galp)
table(isProperPair(galp))
seqlevels(galp)

## Rename the reference sequences:
seqlevels(galp) <- sub("seq", "chr", seqlevels(galp))
seqlevels(galp)

galp[[1]]
unlist(galp)

grglist(galp)  # a GRangesList object
grglist(galp, order.as.in.query=TRUE)
stopifnot(identical(unname(elementLengths(grglist(galp))), njunc(galp) + 2L))

granges(galp)  # a GRanges object

Documentation reproduced from package GenomicAlignments, version 1.2.2, License: Artistic-2.0

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