IMPORTANT NOTE: The GAlignmentPairs container only supports pairs where the 2 alignments are on opposite strands of the same chromosome at the moment. This will change in BioC 3.4.
GAlignmentPairs(first, last, strandMode=1,
isProperPair=TRUE, names=NULL):
Low-level GAlignmentPairs constructor. Generally not used directly.
x is a GAlignmentPairs object. strandMode(x), strandMode(x) <- value:
The strand mode is a per-object switch on GAlignmentPairs objects
that controls the behavior of the strand getter.
More precisely, it indicates how the strand of a pair should be
inferred from the strand of the first and last alignments in the pair:
strandSpecific equal 0, 1, and 2,
respectively, for the featureCounts function defined in the
Rsubread package. Note that, by default, the readGAlignmentPairs function
sets the strand mode to 1 on the returned GAlignmentPairs object. The
function has a strandMode argument to let the user set a different
strand mode. The strand mode can also be changed any time with the
strandMode setter. Also note that 3rd party programs TopHat2 and Cufflinks have a
--library-type option to let the user specify which protocol
was used. Please refer to the documentation of these programs for more
information.
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, real.strand=FALSE),
last(x, real.strand=FALSE):
second(x, real.strand=FALSE):
Get the "first" or "last"/"second" alignment for each alignment pair in
x. The result is a GAlignments object of the same length
as x. If real.strand=TRUE, then the strand is inverted on-the-fly
according to the strand mode currently set on the object (see
strandMode(x) above). More precisely, if strandMode(x)
is 0, then the strand is set to * for the GAlignments object
returned by both, first() and last().
If strandMode(x) is 1, then the strand of the object returned
by last() is inverted. If strandMode(x) is 2, then the
strand of the object returned by first() is 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 (readGAlignmentPairs, the function used for reading
paired-end reads from a BAM file as a GAlignmentPairs object, rejects
pairs with incompatible RNAME values).
strand(x), strand(x) <- value:
Get or set the strand for each alignment pair in x.
Obeys strandMode(x) above to infer the strand of a pair.
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.
x is a GAlignmentPairs object. x[i]:
Return a new GAlignmentPairs object made of the selected
alignment pairs.
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.
x is a GAlignmentPairs object. granges(x, use.names=TRUE, use.mcols=FALSE),
ranges(x, use.names=TRUE, use.mcols=FALSE): Return a GRanges object (for granges()) or
IRanges) object (for ranges()) parallel
to x where the i-th element is the range of the genomic region
spanned by the i-th alignment in x. All gaps in the region are
ignored. If use.names is TRUE, then the names on x
(if any) are propagated to the returned object.
If use.mcols is TRUE, then the metadata columns on x
(if any) are propagated to the returned object.
grglist(x, use.mcols=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. The strand of
the returned ranges obeys the strand mode currently set on the
object (see strandMode(x) above). More precisely, if grl1 and grl2 are
grglist(first(x, real.strand=TRUE), order.as.in.query=TRUE) and
grglist(last(x, real.strand=TRUE), order.as.in.query=TRUE),
respectively, then the i-th element in the returned GRangesList
object is c(grl1[[i]], grl2[[i]]), if strandMode(x) is 1,
or c(grl2[[i]], grl1[[i]]), if strandMode(x) is 2. Note that this results in the ranges being always ordered
consistently with the original "query template", that is, being in the
order defined by walking the "query template" from the beginning to
the end. If use.names is TRUE, then the names on x
(if any) are propagated to the returned object.
If use.mcols is TRUE, then the metadata columns on x
(if any) are propagated to the returned object. 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.
as(x, "GRanges"), as(x, "Ranges"),
as(x, "GRangesList"):
Alternate ways of doing
granges(x, use.names=TRUE, use.mcols=TRUE),
ranges(x, use.names=TRUE, use.mcols=TRUE), and
grglist(x, use.names=TRUE, use.mcols=TRUE), respectively.
as(x, "GAlignments"):
Equivalent of unlist(x, use.names=TRUE).
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).
An "alignment pair" is made of a "first" and a "last"/"second" 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.
readGAlignmentPairs for reading aligned paired-end
reads from a file (typically a BAM file) into a GAlignmentPairs
object.
makeGAlignmentPairs for pairing the elements of a
GAlignments object into a GAlignmentPairs object.
seqinfo in the GenomeInfoDb
package for getting/setting/modifying the sequence information
stored in an object.
library(Rsamtools) # for the ex1.bam file
ex1_file <- system.file("extdata", "ex1.bam", package="Rsamtools")
galp <- readGAlignmentPairs(ex1_file, use.names=TRUE, strandMode=1)
galp
length(galp)
head(galp)
head(names(galp))
first(galp)
last(galp)
# or
second(galp)
strandMode(galp)
first(galp, real.strand=TRUE)
last(galp, real.strand=TRUE)
strand(galp)
strandMode(galp) <- 2
first(galp, real.strand=TRUE)
last(galp, real.strand=TRUE)
strand(galp)
seqnames(galp)
head(njunc(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
strandMode(galp) <- 1
grglist(galp)
stopifnot(identical(unname(elementNROWS(grglist(galp))), njunc(galp) + 2L))
granges(galp) # a GRanges object
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