intra-range-methods: Intra range transformations of a GRanges or GRangesList...
In GenomicRanges: Representation and manipulation of genomic intervals
Description
Usage
Arguments
Details
Author(s)
See Also
Examples
Description
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.
Usage
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## 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)
Arguments
x
A GenomicRanges object.
shift, use.names, start, end, width, both, fix, keep.all.ranges,
upstream, downstream
See ?`intra-range-methods`.
ignore.strand
TRUE or FALSE. Whether the strand of the input ranges
should be ignored or not. See details below.
Details
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.
Author(s)
P. Aboyoun and V. Obenchain
See Also
-
GenomicRanges, GRanges, and GRangesList objects.
The intra-range-methods man page in the
IRanges package.
The IntegerRanges class in the IRanges package.
Examples
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## ---------------------------------------------------------------------
## 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)
Example output
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, basename, cbind, colnames,
dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:base’:
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
GRanges object with 10 ranges and 2 metadata columns:
seqnames ranges strand | score GC
<Rle> <IRanges> <Rle> | <integer> <numeric>
a chr1 1-10 - | 1 1.000000
b chr2 2-10 + | 2 0.888889
c chr2 3-10 + | 3 0.777778
d chr2 4-10 * | 4 0.666667
e chr1 5-10 * | 5 0.555556
f chr1 6-10 + | 6 0.444444
g chr3 7-10 + | 7 0.333333
h chr3 8-10 + | 8 0.222222
i chr3 9-10 - | 9 0.111111
j chr3 10 - | 10 0.000000
-------
seqinfo: 3 sequences from an unspecified genome; no seqlengths
GRanges object with 10 ranges and 2 metadata columns:
seqnames ranges strand | score GC
<Rle> <IRanges> <Rle> | <integer> <numeric>
a chr1 2-11 - | 1 1.000000
b chr2 3-11 + | 2 0.888889
c chr2 4-11 + | 3 0.777778
d chr2 5-11 * | 4 0.666667
e chr1 6-11 * | 5 0.555556
f chr1 7-11 + | 6 0.444444
g chr3 8-11 + | 7 0.333333
h chr3 9-11 + | 8 0.222222
i chr3 10-11 - | 9 0.111111
j chr3 11 - | 10 0.000000
-------
seqinfo: 3 sequences from an unspecified genome; no seqlengths
GRanges object with 9 ranges and 2 metadata columns:
seqnames ranges strand | score GC
<Rle> <IRanges> <Rle> | <integer> <numeric>
a chr1 2-9 - | 1 1.000000
b chr2 3-9 + | 2 0.888889
c chr2 4-9 + | 3 0.777778
d chr2 5-9 * | 4 0.666667
e chr1 6-9 * | 5 0.555556
f chr1 7-9 + | 6 0.444444
g chr3 8-9 + | 7 0.333333
h chr3 9 + | 8 0.222222
i chr3 10-9 - | 9 0.111111
-------
seqinfo: 3 sequences from an unspecified genome; no seqlengths
GRanges object with 10 ranges and 2 metadata columns:
seqnames ranges strand | score GC
<Rle> <IRanges> <Rle> | <integer> <numeric>
a chr1 1-10 - | 1 1.000000
b chr2 2-11 + | 2 0.888889
c chr2 3-12 + | 3 0.777778
d chr2 4-13 * | 4 0.666667
e chr1 5-14 * | 5 0.555556
f chr1 6-15 + | 6 0.444444
g chr3 7-16 + | 7 0.333333
h chr3 8-17 + | 8 0.222222
i chr3 1-10 - | 9 0.111111
j chr3 1-10 - | 10 0.000000
-------
seqinfo: 3 sequences from an unspecified genome; no seqlengths
GRanges object with 10 ranges and 2 metadata columns:
seqnames ranges strand | score GC
<Rle> <IRanges> <Rle> | <integer> <numeric>
a chr1 11-20 - | 1 1.000000
b chr2 -8-1 + | 2 0.888889
c chr2 -7-2 + | 3 0.777778
d chr2 -6-3 * | 4 0.666667
e chr1 -5-4 * | 5 0.555556
f chr1 -4-5 + | 6 0.444444
g chr3 -3-6 + | 7 0.333333
h chr3 -2-7 + | 8 0.222222
i chr3 11-20 - | 9 0.111111
j chr3 11-20 - | 10 0.000000
-------
seqinfo: 3 sequences from an unspecified genome; no seqlengths
GRanges object with 8 ranges and 2 metadata columns:
seqnames ranges strand | score GC
<Rle> <IRanges> <Rle> | <integer> <numeric>
a chr1 3-7 - | 1 1.000000
b chr2 3-7 + | 2 0.888889
c chr2 3-7 + | 3 0.777778
d chr2 4-7 * | 4 0.666667
e chr1 5-7 * | 5 0.555556
f chr1 6-7 + | 6 0.444444
g chr3 7 + | 7 0.333333
h chr3 8-7 + | 8 0.222222
-------
seqinfo: 3 sequences from an unspecified genome; no seqlengths
GRanges object with 3 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chr1 8-11 +
[2] chr1 14-17 -
[3] chr1 8-11 *
-------
seqinfo: 1 sequence from an unspecified genome; no seqlengths
GRangesList object of length 3:
$gr1
GRanges object with 1 range and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chr2 3-6 *
-------
seqinfo: 2 sequences from an unspecified genome; no seqlengths
$gr2
GRanges object with 2 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chr1 7-9 +
[2] chr1 13-15 -
-------
seqinfo: 2 sequences from an unspecified genome; no seqlengths
$gr3
GRanges object with 2 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chr1 1-3 -
[2] chr2 4-9 -
-------
seqinfo: 2 sequences from an unspecified genome; no seqlengths
GRangesList object of length 3:
$gr1
GRanges object with 1 range and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chr2 3-22 *
-------
seqinfo: 2 sequences from an unspecified genome; no seqlengths
$gr2
GRanges object with 2 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chr1 7-26 +
[2] chr1 -4-15 -
-------
seqinfo: 2 sequences from an unspecified genome; no seqlengths
$gr3
GRanges object with 2 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chr1 -16-3 -
[2] chr2 -10-9 -
-------
seqinfo: 2 sequences from an unspecified genome; no seqlengths
GRangesList object of length 3:
$gr1
GRanges object with 1 range and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chr2 -17-2 *
-------
seqinfo: 2 sequences from an unspecified genome; no seqlengths
$gr2
GRanges object with 2 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chr1 -13-6 +
[2] chr1 16-35 -
-------
seqinfo: 2 sequences from an unspecified genome; no seqlengths
$gr3
GRanges object with 2 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chr1 4-23 -
[2] chr2 10-29 -
-------
seqinfo: 2 sequences from an unspecified genome; no seqlengths
GRangesList object of length 3:
$gr1
GRanges object with 1 range and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chr2 3-6 *
-------
seqinfo: 2 sequences from an unspecified genome; no seqlengths
$gr2
GRanges object with 2 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chr1 7-9 +
[2] chr1 13-15 -
-------
seqinfo: 2 sequences from an unspecified genome; no seqlengths
$gr3
GRanges object with 2 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chr1 3 -
[2] chr2 4-9 -
-------
seqinfo: 2 sequences from an unspecified genome; no seqlengths
GenomicRanges documentation built on Nov. 8, 2020, 5:46 p.m.
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Description Usage Arguments Details Author(s) See Also Examples
Description
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.
Usage
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 | ## 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)
|
Arguments
x |
A GenomicRanges object. |
shift, use.names, start, end, width, both, fix, keep.all.ranges,
upstream, downstream |
See |
ignore.strand |
|
Details
shiftbehaves like theshiftmethod for IntegerRanges objects. See?`intra-range-methods`for the details.narrowon 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.resizereturns an object of the same type and length asxcontaining intervals that have been resized to widthwidthbased on thestrand(x)values. Elements wherestrand(x) == "+"orstrand(x) == "*"are anchored atstart(x)and elements wherestrand(x) == "-"are anchored at theend(x). Theuse.namesargument determines whether or not to keep the names on the ranges.flankreturns an object of the same type and length asxcontaining intervals of widthwidththat flank the intervals inx. Thestartargument takes a logical indicating whetherxshould be flanked at the "start" (TRUE) or the "end" (FALSE), which forstrand(x) != "-"isstart(x)andend(x)respectively and forstrand(x) == "-"isend(x)andstart(x)respectively. Thebothargument takes a single logical value indicating whether the flanking regionwidthpositions extends into the range. Ifboth=TRUE, the resulting range thus straddles the end point, withwidthpositions on either side.-
promotersreturns an object of the same type and length asxcontaining promoter ranges. Promoter ranges extend around the transcription start site (TSS) which is defined asstart(x)for ranges on the+or*strand and asend(x)for ranges on the-strand. Theupstreamanddownstreamarguments 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.
restrictreturns an object of the same type and length asxcontaining restricted ranges for distinct seqnames. Thestartandendarguments 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 inx. See?`intra-range-methods`for more information about range restriction and for a description of the optional arguments.trimtrims out-of-bound ranges located on non-circular sequences whose length is not NA.
Author(s)
P. Aboyoun and V. Obenchain
See Also
-
GenomicRanges, GRanges, and GRangesList objects.
The intra-range-methods man page in the IRanges package.
The IntegerRanges class in the IRanges package.
Examples
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)
|
Example output
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, basename, cbind, colnames,
dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:base’:
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
GRanges object with 10 ranges and 2 metadata columns:
seqnames ranges strand | score GC
<Rle> <IRanges> <Rle> | <integer> <numeric>
a chr1 1-10 - | 1 1.000000
b chr2 2-10 + | 2 0.888889
c chr2 3-10 + | 3 0.777778
d chr2 4-10 * | 4 0.666667
e chr1 5-10 * | 5 0.555556
f chr1 6-10 + | 6 0.444444
g chr3 7-10 + | 7 0.333333
h chr3 8-10 + | 8 0.222222
i chr3 9-10 - | 9 0.111111
j chr3 10 - | 10 0.000000
-------
seqinfo: 3 sequences from an unspecified genome; no seqlengths
GRanges object with 10 ranges and 2 metadata columns:
seqnames ranges strand | score GC
<Rle> <IRanges> <Rle> | <integer> <numeric>
a chr1 2-11 - | 1 1.000000
b chr2 3-11 + | 2 0.888889
c chr2 4-11 + | 3 0.777778
d chr2 5-11 * | 4 0.666667
e chr1 6-11 * | 5 0.555556
f chr1 7-11 + | 6 0.444444
g chr3 8-11 + | 7 0.333333
h chr3 9-11 + | 8 0.222222
i chr3 10-11 - | 9 0.111111
j chr3 11 - | 10 0.000000
-------
seqinfo: 3 sequences from an unspecified genome; no seqlengths
GRanges object with 9 ranges and 2 metadata columns:
seqnames ranges strand | score GC
<Rle> <IRanges> <Rle> | <integer> <numeric>
a chr1 2-9 - | 1 1.000000
b chr2 3-9 + | 2 0.888889
c chr2 4-9 + | 3 0.777778
d chr2 5-9 * | 4 0.666667
e chr1 6-9 * | 5 0.555556
f chr1 7-9 + | 6 0.444444
g chr3 8-9 + | 7 0.333333
h chr3 9 + | 8 0.222222
i chr3 10-9 - | 9 0.111111
-------
seqinfo: 3 sequences from an unspecified genome; no seqlengths
GRanges object with 10 ranges and 2 metadata columns:
seqnames ranges strand | score GC
<Rle> <IRanges> <Rle> | <integer> <numeric>
a chr1 1-10 - | 1 1.000000
b chr2 2-11 + | 2 0.888889
c chr2 3-12 + | 3 0.777778
d chr2 4-13 * | 4 0.666667
e chr1 5-14 * | 5 0.555556
f chr1 6-15 + | 6 0.444444
g chr3 7-16 + | 7 0.333333
h chr3 8-17 + | 8 0.222222
i chr3 1-10 - | 9 0.111111
j chr3 1-10 - | 10 0.000000
-------
seqinfo: 3 sequences from an unspecified genome; no seqlengths
GRanges object with 10 ranges and 2 metadata columns:
seqnames ranges strand | score GC
<Rle> <IRanges> <Rle> | <integer> <numeric>
a chr1 11-20 - | 1 1.000000
b chr2 -8-1 + | 2 0.888889
c chr2 -7-2 + | 3 0.777778
d chr2 -6-3 * | 4 0.666667
e chr1 -5-4 * | 5 0.555556
f chr1 -4-5 + | 6 0.444444
g chr3 -3-6 + | 7 0.333333
h chr3 -2-7 + | 8 0.222222
i chr3 11-20 - | 9 0.111111
j chr3 11-20 - | 10 0.000000
-------
seqinfo: 3 sequences from an unspecified genome; no seqlengths
GRanges object with 8 ranges and 2 metadata columns:
seqnames ranges strand | score GC
<Rle> <IRanges> <Rle> | <integer> <numeric>
a chr1 3-7 - | 1 1.000000
b chr2 3-7 + | 2 0.888889
c chr2 3-7 + | 3 0.777778
d chr2 4-7 * | 4 0.666667
e chr1 5-7 * | 5 0.555556
f chr1 6-7 + | 6 0.444444
g chr3 7 + | 7 0.333333
h chr3 8-7 + | 8 0.222222
-------
seqinfo: 3 sequences from an unspecified genome; no seqlengths
GRanges object with 3 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chr1 8-11 +
[2] chr1 14-17 -
[3] chr1 8-11 *
-------
seqinfo: 1 sequence from an unspecified genome; no seqlengths
GRangesList object of length 3:
$gr1
GRanges object with 1 range and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chr2 3-6 *
-------
seqinfo: 2 sequences from an unspecified genome; no seqlengths
$gr2
GRanges object with 2 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chr1 7-9 +
[2] chr1 13-15 -
-------
seqinfo: 2 sequences from an unspecified genome; no seqlengths
$gr3
GRanges object with 2 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chr1 1-3 -
[2] chr2 4-9 -
-------
seqinfo: 2 sequences from an unspecified genome; no seqlengths
GRangesList object of length 3:
$gr1
GRanges object with 1 range and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chr2 3-22 *
-------
seqinfo: 2 sequences from an unspecified genome; no seqlengths
$gr2
GRanges object with 2 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chr1 7-26 +
[2] chr1 -4-15 -
-------
seqinfo: 2 sequences from an unspecified genome; no seqlengths
$gr3
GRanges object with 2 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chr1 -16-3 -
[2] chr2 -10-9 -
-------
seqinfo: 2 sequences from an unspecified genome; no seqlengths
GRangesList object of length 3:
$gr1
GRanges object with 1 range and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chr2 -17-2 *
-------
seqinfo: 2 sequences from an unspecified genome; no seqlengths
$gr2
GRanges object with 2 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chr1 -13-6 +
[2] chr1 16-35 -
-------
seqinfo: 2 sequences from an unspecified genome; no seqlengths
$gr3
GRanges object with 2 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chr1 4-23 -
[2] chr2 10-29 -
-------
seqinfo: 2 sequences from an unspecified genome; no seqlengths
GRangesList object of length 3:
$gr1
GRanges object with 1 range and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chr2 3-6 *
-------
seqinfo: 2 sequences from an unspecified genome; no seqlengths
$gr2
GRanges object with 2 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chr1 7-9 +
[2] chr1 13-15 -
-------
seqinfo: 2 sequences from an unspecified genome; no seqlengths
$gr3
GRanges object with 2 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chr1 3 -
[2] chr2 4-9 -
-------
seqinfo: 2 sequences from an unspecified genome; no seqlengths
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