Description Usage Arguments Details Author(s) See Also Examples
This man page documents intra range transformations of a GenomicRanges object (i.e. of an object that belongs to the GenomicRanges class or one of its subclasses, this includes for example GRanges objects), or a GRangesList object.
See ?`intra-range-methods`
and
?`inter-range-methods`
in the IRanges
package for a quick introduction to intra range and inter
range transformations.
Intra range methods for GAlignments and GAlignmentsList objects are defined and documented in the GenomicAlignments package.
See ?`inter-range-methods`
for
inter range transformations of a GenomicRanges or
GRangesList object.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 | ## S4 method for signature 'GenomicRanges'
shift(x, shift=0L, use.names=TRUE)
## S4 method for signature 'GRangesList'
shift(x, shift=0L, use.names=TRUE)
## S4 method for signature 'GenomicRangesList'
shift(x, shift=0L, use.names=TRUE)
## S4 method for signature 'GenomicRanges'
narrow(x, start=NA, end=NA, width=NA, use.names=TRUE)
## S4 method for signature 'GRangesList'
narrow(x, start=NA, end=NA, width=NA, use.names=TRUE)
## S4 method for signature 'GenomicRangesList'
narrow(x, start=NA, end=NA, width=NA,
use.names=TRUE)
## S4 method for signature 'GenomicRanges'
resize(x, width, fix="start", use.names=TRUE,
ignore.strand=FALSE)
## S4 method for signature 'GRangesList'
resize(x, width, fix="start", use.names=TRUE,
ignore.strand=FALSE)
## S4 method for signature 'GenomicRangesList'
resize(x, width, fix="start", use.names=TRUE,
ignore.strand=FALSE)
## S4 method for signature 'GenomicRanges'
flank(x, width, start=TRUE, both=FALSE,
use.names=TRUE, ignore.strand=FALSE)
## S4 method for signature 'GRangesList'
flank(x, width, start=TRUE, both=FALSE,
use.names=TRUE, ignore.strand=FALSE)
## S4 method for signature 'GenomicRangesList'
flank(x, width, start=TRUE, both=FALSE,
use.names=TRUE, ignore.strand=FALSE)
## S4 method for signature 'GenomicRanges'
promoters(x, upstream=2000, downstream=200)
## S4 method for signature 'GRangesList'
promoters(x, upstream=2000, downstream=200)
## S4 method for signature 'GenomicRangesList'
promoters(x, upstream=2000, downstream=200)
## S4 method for signature 'GenomicRanges'
restrict(x, start=NA, end=NA, keep.all.ranges=FALSE,
use.names=TRUE)
## S4 method for signature 'GRangesList'
restrict(x, start=NA, end=NA, keep.all.ranges=FALSE,
use.names=TRUE)
## S4 method for signature 'GenomicRangesList'
restrict(x, start=NA, end=NA,
keep.all.ranges=FALSE, use.names=TRUE)
## S4 method for signature 'GenomicRanges'
trim(x, use.names=TRUE)
|
x |
A GenomicRanges or GRangesList object. |
shift, use.names, start, end, width, both, fix, keep.all.ranges,
upstream, downstream |
See |
ignore.strand |
|
... |
Additional arguments to methods. |
shift
behaves like the shift
method for
Ranges objects. See
?`intra-range-methods`
for the details.
()narrow
on a GenomicRanges object behaves
like on a Ranges object. See
?`intra-range-methods`
for the details.
A major difference though is that it returns a GenomicRanges
object instead of a Ranges object.
The returned object is parallel (i.e. same length and names)
to the original object x
.
resize
returns an object of the same type and length as
x
containing intervals that have been resized to width
width
based on the strand(x)
values. Elements where
strand(x) == "+"
or strand(x) == "*"
are anchored at
start(x)
and elements where strand(x) == "-"
are anchored
at the end(x)
. The use.names
argument determines whether
or not to keep the names on the ranges.
flank
returns an object of the same type and length
as x
containing intervals of width width
that flank
the intervals in x
. The start
argument takes a
logical indicating whether x
should be flanked at the
"start" (TRUE
) or the "end" (FALSE
), which for
strand(x) != "-"
is start(x)
and end(x)
respectively and for strand(x) == "-"
is end(x)
and
start(x)
respectively. The both
argument takes a
single logical value indicating whether the flanking region
width
positions extends into the range. If
both=TRUE
, the resulting range thus straddles the end
point, with width
positions on either side.
promoters
returns an object of the same type and length
as x
containing promoter ranges. Promoter ranges extend
around the transcription start site (TSS) which is defined as
start(x)
. The upsteam
and downstream
arguments
define the number of nucleotides in the 5' and 3' direction,
respectively. The full range is defined as,
(start(x) - upstream) to (start(x) + downstream - 1).
Ranges on the *
strand are treated the same as those on the
+
strand. When no seqlengths are present in x
, it is
possible to have non-positive start values in the promoter ranges. This
occurs when (TSS - upstream
) < 1. In the equal but opposite case,
the end
values of the ranges may extend beyond the chromosome end
when (TSS + downstream
+ 1) > 'chromosome end'. When
seqlengths
are not NA
the promoter ranges are kept within
the bounds of the defined seqlengths
.
restrict
returns an object of the same type and length as
x
containing restricted ranges for distinct seqnames. The
start
and end
arguments can be a named numeric vector of
seqnames for the ranges to be resticted or a numeric vector or length 1
if the restriction operation is to be applied to all the sequences in
x
. See ?`intra-range-methods`
for more
information about range restriction and for a description of the optional
arguments.
trim
trims out-of-bound ranges located on non-circular
sequences whose length is not NA.
P. Aboyoun and V. Obenchain <[email protected]>
GenomicRanges, GRanges, and GRangesList objects.
The intra-range-methods man page in the IRanges package.
The Ranges class in the IRanges package.
endoapply
in the S4Vectors package.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 | ## ---------------------------------------------------------------------
## A. ON A GRanges OBJECT
## ---------------------------------------------------------------------
gr <- GRanges(
seqnames=Rle(paste("chr", c(1, 2, 1, 3), sep=""), c(1, 3, 2, 4)),
ranges=IRanges(1:10, width=10:1, names=letters[1:10]),
strand=Rle(strand(c("-", "+", "*", "+", "-")), c(1, 2, 2, 3, 2)),
score=1:10,
GC=seq(1, 0, length=10)
)
gr
shift(gr, 1)
narrow(gr[-10], start=2, end=-2)
resize(gr, width=10)
flank(gr, width=10)
restrict(gr, start=3, end=7)
gr <- GRanges("chr1", IRanges(rep(10, 3), width=6), c("+", "-", "*"))
promoters(gr, 2, 2)
## ---------------------------------------------------------------------
## B. ON A GRangesList OBJECT
## ---------------------------------------------------------------------
gr1 <- GRanges("chr2", IRanges(3, 6))
gr2 <- GRanges(c("chr1", "chr1"), IRanges(c(7,13), width=3),
strand=c("+", "-"))
gr3 <- GRanges(c("chr1", "chr2"), IRanges(c(1, 4), c(3, 9)),
strand="-")
grl <- GRangesList(gr1= gr1, gr2=gr2, gr3=gr3)
grl
resize(grl, width=20)
flank(grl, width=20)
restrict(grl, start=3)
|
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