Intra range transformations of a GRanges or GRangesList object
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.
## S4 method for signature 'GenomicRanges'
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 'GenomicRanges'
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 'GenomicRanges'
promoters(x, upstream=2000, downstream=200, use.names=TRUE)
## S4 method for signature 'GenomicRanges'
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 object. |
shift, use.names, start, end, width, both, fix, keep.all.ranges,
upstream, downstream |
See |
ignore.strand |
|
shift behaves like the shift method for
IntegerRanges objects. See
?`intra-range-methods` for the details.
narrow on a GenomicRanges object behaves
like on an IntegerRanges object. See
?`intra-range-methods` for the details.
A major difference though is that it returns a GenomicRanges
object instead of an IntegerRanges 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) for ranges on the + or * strand
and as end(x) for ranges on the - strand.
The upstream and downstream arguments define the
number of nucleotides in the 5' and 3' direction, respectively.
More precisely, the output range is defined as
(start(x) - upstream) to (start(x) + downstream - 1)
for ranges on the + or * strand, and as
(end(x) - downstream + 1) to (end(x) + upstream)
for ranges on the - strand.
Note that the returned object might contain out-of-bound ranges i.e. ranges that start before the first nucleotide position and/or end after the last nucleotide position of the underlying sequence.
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
GenomicRanges, GRanges, and GRangesList objects.
The intra-range-methods man page in the IRanges package.
The IntegerRanges class in the IRanges package.
## ---------------------------------------------------------------------
## 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)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.