extractListFragments: Extract list fragments from a list-like object
In IRanges: Foundation of integer range manipulation in Bioconductor
Description
Usage
Arguments
Details
Value
Author(s)
See Also
Examples
View source: R/extractListFragments.R
Description
Utilities for extracting list fragments from a list-like object.
Usage
1
2
3
4
extractListFragments(x, aranges, use.mcols=FALSE,
msg.if.incompatible=INCOMPATIBLE_ARANGES_MSG)
equisplit(x, nchunk, chunksize, use.mcols=FALSE)
Arguments
x
The list-like object from which to extract the list fragments.
Can be any List derivative for extractListFragments.
Can also be an ordinary list if extractListFragments is
called with use.mcols=TRUE.
Can be any List derivative that supports relist()
for equisplit.
aranges
An IntegerRanges derivative containing the absolute ranges
(i.e. the ranges along unlist(x)) of the list fragments
to extract.
The ranges in aranges must be compatible with the
cumulated length of all the list elements in x,
that is, start(aranges) and end(aranges) must
be >= 1 and <= sum(elementNROWS(x)), respectively.
Also please note that only IntegerRanges objects that are
disjoint and sorted are supported at the moment.
use.mcols
Whether to propagate the metadata columns on x (if any) or not.
Must be TRUE or FALSE (the default).
If set to FALSE, instead of having the metadata columns propagated
from x, the object returned by extractListFragments has
metadata columns revmap and revmap2, and the object
returned by equisplit has metadata column revmap. Note that
this is the default.
msg.if.incompatible
The error message to use if aranges is not compatible with
the cumulated length of all the list elements in x.
nchunk
The number of chunks. Must be a single positive integer.
chunksize
The size of the chunks (last chunk might be smaller). Must be a single
positive integer.
Details
A list fragment of list-like object x is a window in one of
its list elements.
extractListFragments is a low-level utility that extracts list
fragments from list-like object x according to the absolute ranges
in aranges.
equisplit fragments and splits list-like object x into a
specified number of partitions with equal (total) width. This is useful
for instance to ensure balanced loading of workers in parallel evaluation.
For example, if x is a GRanges object,
each partition is also a GRanges object and the
set of all partitions is returned as a GRangesList
object.
Value
An object of the same class as x for extractListFragments.
An object of class relistToClass(x) for
equisplit.
Author(s)
Hervé Pagès
See Also
-
IRanges and IRangesList objects.
-
Partitioning objects.
-
IntegerList objects.
-
breakInChunks from breaking a vector-like object
in chunks.
-
GRanges and GRangesList
objects defined in the GenomicRanges package.
-
List objects defined in the S4Vectors
package.
-
intra-range-methods and inter-range-methods
for intra range and inter range transformations.
Examples
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## ---------------------------------------------------------------------
## A. extractListFragments()
## ---------------------------------------------------------------------
x <- IntegerList(a=101:109, b=5:-5)
x
aranges <- IRanges(start=c(2, 4, 8, 17, 17), end=c(3, 6, 14, 16, 19))
aranges
extractListFragments(x, aranges)
x2 <- IRanges(c(1, 101, 1001, 10001), width=c(10, 5, 0, 12),
names=letters[1:4])
mcols(x2)$label <- LETTERS[1:4]
x2
aranges <- IRanges(start=13, end=20)
extractListFragments(x2, aranges)
extractListFragments(x2, aranges, use.mcols=TRUE)
aranges2 <- PartitioningByWidth(c(3, 9, 13, 0, 2))
extractListFragments(x2, aranges2)
extractListFragments(x2, aranges2, use.mcols=TRUE)
x2b <- as(x2, "IntegerList")
extractListFragments(x2b, aranges2)
x2c <- as.list(x2b)
extractListFragments(x2c, aranges2, use.mcols=TRUE)
## ---------------------------------------------------------------------
## B. equisplit()
## ---------------------------------------------------------------------
## equisplit() first calls breakInChunks() internally to create a
## PartitioningByWidth object that contains the absolute ranges of the
## chunks, then calls extractListFragments() on it 'x' to extract the
## fragments of 'x' that correspond to these absolute ranges. Finally
## the IRanges object returned by extractListFragments() is split into
## an IRangesList object where each list element corresponds to a chunk.
equisplit(x2, nchunk=2)
equisplit(x2, nchunk=2, use.mcols=TRUE)
equisplit(x2, chunksize=5)
library(GenomicRanges)
gr <- GRanges(c("chr1", "chr2"), IRanges(1, c(100, 1e5)))
equisplit(gr, nchunk=2)
equisplit(gr, nchunk=1000)
## ---------------------------------------------------------------------
## C. ADVANCED extractListFragments() EXAMPLES
## ---------------------------------------------------------------------
## === D1. Fragment list-like object into length 1 fragments ===
## First we construct a Partitioning object where all the partitions
## have a width of 1:
x2_cumlen <- nobj(PartitioningByWidth(x2)) # Equivalent to
# length(unlist(x2)) except
# that it doesn't unlist 'x2'
# so is much more efficient.
aranges1 <- PartitioningByEnd(seq_len(x2_cumlen))
aranges1
## Then we use it to fragment 'x2':
extractListFragments(x2, aranges1)
extractListFragments(x2b, aranges1)
extractListFragments(x2c, aranges1, use.mcols=TRUE)
## === D2. Fragment a Partitioning object ===
partitioning2 <- PartitioningByEnd(x2b) # same as PartitioningByEnd(x2)
extractListFragments(partitioning2, aranges2)
## Note that when the 1st arg is a Partitioning derivative, then
## swapping the 1st and 2nd elements in the call to extractListFragments()
## doesn't change the returned partitioning:
extractListFragments(aranges2, partitioning2)
## ---------------------------------------------------------------------
## D. SANITY CHECKS
## ---------------------------------------------------------------------
## If 'aranges' is 'PartitioningByEnd(x)' or 'PartitioningByWidth(x)'
## and 'x' has no zero-length list elements, then
## 'extractListFragments(x, aranges, use.mcols=TRUE)' is a no-op.
check_no_ops <- function(x) {
aranges <- PartitioningByEnd(x)
stopifnot(identical(
extractListFragments(x, aranges, use.mcols=TRUE), x
))
aranges <- PartitioningByWidth(x)
stopifnot(identical(
extractListFragments(x, aranges, use.mcols=TRUE), x
))
}
check_no_ops(x2[lengths(x2) != 0])
check_no_ops(x2b[lengths(x2b) != 0])
check_no_ops(x2c[lengths(x2c) != 0])
check_no_ops(gr)
Example output
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':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
IntegerList of length 2
[["a"]] 101 102 103 104 105 106 107 108 109
[["b"]] 5 4 3 2 1 0 -1 -2 -3 -4 -5
IRanges object with 5 ranges and 0 metadata columns:
start end width
<integer> <integer> <integer>
[1] 2 3 2
[2] 4 6 3
[3] 8 14 7
[4] 17 16 0
[5] 17 19 3
IntegerList of length 6
[["a"]] 102 103
[["a"]] 104 105 106
[["a"]] 108 109
[["b"]] 5 4 3 2 1
[["b"]] integer(0)
[["b"]] -2 -3 -4
IRanges object with 4 ranges and 1 metadata column:
start end width | label
<integer> <integer> <integer> | <character>
a 1 10 10 | A
b 101 105 5 | B
c 1001 1000 0 | C
d 10001 10012 12 | D
IRanges object with 3 ranges and 2 metadata columns:
start end width | revmap revmap2
<integer> <integer> <integer> | <integer> <integer>
b 103 105 3 | 2 1
c 1001 1000 0 | 3 1
d 10001 10005 5 | 4 1
IRanges object with 3 ranges and 1 metadata column:
start end width | label
<integer> <integer> <integer> | <character>
b 103 105 3 | B
c 1001 1000 0 | C
d 10001 10005 5 | D
IRanges object with 8 ranges and 2 metadata columns:
start end width | revmap revmap2
<integer> <integer> <integer> | <integer> <integer>
a 1 3 3 | 1 1
a 4 10 7 | 1 2
b 101 102 2 | 2 2
b 103 105 3 | 2 3
c 1001 1000 0 | 3 3
d 10001 10010 10 | 4 3
d 10011 10010 0 | 4 4
d 10011 10012 2 | 4 5
IRanges object with 8 ranges and 1 metadata column:
start end width | label
<integer> <integer> <integer> | <character>
a 1 3 3 | A
a 4 10 7 | A
b 101 102 2 | B
b 103 105 3 | B
c 1001 1000 0 | C
d 10001 10010 10 | D
d 10011 10010 0 | D
d 10011 10012 2 | D
IntegerList of length 8
[["a"]] 1 2 3
[["a"]] 4 5 6 7 8 9 10
[["b"]] 101 102
[["b"]] 103 104 105
[["c"]] integer(0)
[["d"]] 10001 10002 10003 10004 10005 10006 10007 10008 10009 10010
[["d"]] integer(0)
[["d"]] 10011 10012
$a
[1] 1 2 3
$a
[1] 4 5 6 7 8 9 10
$b
[1] 101 102
$b
[1] 103 104 105
$c
integer(0)
$d
[1] 10001 10002 10003 10004 10005 10006 10007 10008 10009 10010
$d
integer(0)
$d
[1] 10011 10012
IRangesList of length 2
[[1]]
IRanges object with 2 ranges and 1 metadata column:
start end width | revmap
<integer> <integer> <integer> | <integer>
a 1 10 10 | 1
b 101 103 3 | 2
[[2]]
IRanges object with 3 ranges and 1 metadata column:
start end width | revmap
<integer> <integer> <integer> | <integer>
b 104 105 2 | 2
c 1001 1000 0 | 3
d 10001 10012 12 | 4
IRangesList of length 2
[[1]]
IRanges object with 2 ranges and 1 metadata column:
start end width | label
<integer> <integer> <integer> | <character>
a 1 10 10 | A
b 101 103 3 | B
[[2]]
IRanges object with 3 ranges and 1 metadata column:
start end width | label
<integer> <integer> <integer> | <character>
b 104 105 2 | B
c 1001 1000 0 | C
d 10001 10012 12 | D
IRangesList of length 6
[[1]]
IRanges object with 1 range and 1 metadata column:
start end width | revmap
<integer> <integer> <integer> | <integer>
a 1 5 5 | 1
[[2]]
IRanges object with 1 range and 1 metadata column:
start end width | revmap
<integer> <integer> <integer> | <integer>
a 6 10 5 | 1
[[3]]
IRanges object with 1 range and 1 metadata column:
start end width | revmap
<integer> <integer> <integer> | <integer>
b 101 105 5 | 2
...
<3 more elements>
Loading required package: GenomeInfoDb
GRangesList object of length 2:
[[1]]
GRanges object with 2 ranges and 1 metadata column:
seqnames ranges strand | revmap
<Rle> <IRanges> <Rle> | <integer>
[1] chr1 1-100 * | 1
[2] chr2 1-49950 * | 2
[[2]]
GRanges object with 1 range and 1 metadata column:
seqnames ranges strand | revmap
[1] chr2 49951-100000 * | 2
-------
seqinfo: 2 sequences from an unspecified genome; no seqlengths
GRangesList object of length 1000:
[[1]]
GRanges object with 1 range and 1 metadata column:
seqnames ranges strand | revmap
<Rle> <IRanges> <Rle> | <integer>
[1] chr1 1-100 * | 1
[[2]]
GRanges object with 1 range and 1 metadata column:
seqnames ranges strand | revmap
[1] chr2 1-100 * | 2
[[3]]
GRanges object with 1 range and 1 metadata column:
seqnames ranges strand | revmap
[1] chr2 101-200 * | 2
...
<997 more elements>
-------
seqinfo: 2 sequences from an unspecified genome; no seqlengths
PartitioningByEnd object with 27 ranges and 0 metadata columns:
start end width
<integer> <integer> <integer>
[1] 1 1 1
[2] 2 2 1
[3] 3 3 1
[4] 4 4 1
[5] 5 5 1
... ... ... ...
[23] 23 23 1
[24] 24 24 1
[25] 25 25 1
[26] 26 26 1
[27] 27 27 1
IRanges object with 27 ranges and 2 metadata columns:
start end width | revmap revmap2
<integer> <integer> <integer> | <integer> <integer>
a 1 1 1 | 1 1
a 2 2 1 | 1 2
a 3 3 1 | 1 3
a 4 4 1 | 1 4
a 5 5 1 | 1 5
. ... ... ... . ... ...
d 10008 10008 1 | 4 23
d 10009 10009 1 | 4 24
d 10010 10010 1 | 4 25
d 10011 10011 1 | 4 26
d 10012 10012 1 | 4 27
IntegerList of length 27
[["a"]] 1
[["a"]] 2
[["a"]] 3
[["a"]] 4
[["a"]] 5
[["a"]] 6
[["a"]] 7
[["a"]] 8
[["a"]] 9
[["a"]] 10
...
<17 more elements>
$a
[1] 1
$a
[1] 2
$a
[1] 3
$a
[1] 4
$a
[1] 5
$a
[1] 6
$a
[1] 7
$a
[1] 8
$a
[1] 9
$a
[1] 10
$b
[1] 101
$b
[1] 102
$b
[1] 103
$b
[1] 104
$b
[1] 105
$d
[1] 10001
$d
[1] 10002
$d
[1] 10003
$d
[1] 10004
$d
[1] 10005
$d
[1] 10006
$d
[1] 10007
$d
[1] 10008
$d
[1] 10009
$d
[1] 10010
$d
[1] 10011
$d
[1] 10012
PartitioningByEnd object with 8 ranges and 2 metadata columns:
start end width | revmap revmap2
<integer> <integer> <integer> | <integer> <integer>
a 1 3 3 | 1 1
a 4 10 7 | 1 2
b 11 12 2 | 2 2
b 13 15 3 | 2 3
c 16 15 0 | 3 3
d 16 25 10 | 4 3
d 26 25 0 | 4 4
d 26 27 2 | 4 5
PartitioningByWidth object with 8 ranges and 2 metadata columns:
start end width | revmap revmap2
<integer> <integer> <integer> | <integer> <integer>
[1] 1 3 3 | 1 1
[2] 4 10 7 | 2 1
[3] 11 12 2 | 2 2
[4] 13 15 3 | 3 2
[5] 16 15 0 | 3 3
[6] 16 25 10 | 3 4
[7] 26 25 0 | 4 4
[8] 26 27 2 | 5 4
IRanges documentation built on Dec. 14, 2020, 2 a.m.
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Description Usage Arguments Details Value Author(s) See Also Examples
View source: R/extractListFragments.R
Description
Utilities for extracting list fragments from a list-like object.
Usage
1 2 3 4 | extractListFragments(x, aranges, use.mcols=FALSE,
msg.if.incompatible=INCOMPATIBLE_ARANGES_MSG)
equisplit(x, nchunk, chunksize, use.mcols=FALSE)
|
Arguments
x |
The list-like object from which to extract the list fragments. Can be any List derivative for Can be any List derivative that supports |
aranges |
An IntegerRanges derivative containing the absolute ranges
(i.e. the ranges along The ranges in Also please note that only IntegerRanges objects that are disjoint and sorted are supported at the moment. |
use.mcols |
Whether to propagate the metadata columns on Must be |
msg.if.incompatible |
The error message to use if |
nchunk |
The number of chunks. Must be a single positive integer. |
chunksize |
The size of the chunks (last chunk might be smaller). Must be a single positive integer. |
Details
A list fragment of list-like object x is a window in one of
its list elements.
extractListFragments is a low-level utility that extracts list
fragments from list-like object x according to the absolute ranges
in aranges.
equisplit fragments and splits list-like object x into a
specified number of partitions with equal (total) width. This is useful
for instance to ensure balanced loading of workers in parallel evaluation.
For example, if x is a GRanges object,
each partition is also a GRanges object and the
set of all partitions is returned as a GRangesList
object.
Value
An object of the same class as x for extractListFragments.
An object of class relistToClass(x) for
equisplit.
Author(s)
Hervé Pagès
See Also
-
IRanges and IRangesList objects.
-
Partitioning objects.
-
IntegerList objects.
-
breakInChunksfrom breaking a vector-like object in chunks. -
GRanges and GRangesList objects defined in the GenomicRanges package.
-
List objects defined in the S4Vectors package.
-
intra-range-methods and inter-range-methods for intra range and inter range transformations.
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 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 | ## ---------------------------------------------------------------------
## A. extractListFragments()
## ---------------------------------------------------------------------
x <- IntegerList(a=101:109, b=5:-5)
x
aranges <- IRanges(start=c(2, 4, 8, 17, 17), end=c(3, 6, 14, 16, 19))
aranges
extractListFragments(x, aranges)
x2 <- IRanges(c(1, 101, 1001, 10001), width=c(10, 5, 0, 12),
names=letters[1:4])
mcols(x2)$label <- LETTERS[1:4]
x2
aranges <- IRanges(start=13, end=20)
extractListFragments(x2, aranges)
extractListFragments(x2, aranges, use.mcols=TRUE)
aranges2 <- PartitioningByWidth(c(3, 9, 13, 0, 2))
extractListFragments(x2, aranges2)
extractListFragments(x2, aranges2, use.mcols=TRUE)
x2b <- as(x2, "IntegerList")
extractListFragments(x2b, aranges2)
x2c <- as.list(x2b)
extractListFragments(x2c, aranges2, use.mcols=TRUE)
## ---------------------------------------------------------------------
## B. equisplit()
## ---------------------------------------------------------------------
## equisplit() first calls breakInChunks() internally to create a
## PartitioningByWidth object that contains the absolute ranges of the
## chunks, then calls extractListFragments() on it 'x' to extract the
## fragments of 'x' that correspond to these absolute ranges. Finally
## the IRanges object returned by extractListFragments() is split into
## an IRangesList object where each list element corresponds to a chunk.
equisplit(x2, nchunk=2)
equisplit(x2, nchunk=2, use.mcols=TRUE)
equisplit(x2, chunksize=5)
library(GenomicRanges)
gr <- GRanges(c("chr1", "chr2"), IRanges(1, c(100, 1e5)))
equisplit(gr, nchunk=2)
equisplit(gr, nchunk=1000)
## ---------------------------------------------------------------------
## C. ADVANCED extractListFragments() EXAMPLES
## ---------------------------------------------------------------------
## === D1. Fragment list-like object into length 1 fragments ===
## First we construct a Partitioning object where all the partitions
## have a width of 1:
x2_cumlen <- nobj(PartitioningByWidth(x2)) # Equivalent to
# length(unlist(x2)) except
# that it doesn't unlist 'x2'
# so is much more efficient.
aranges1 <- PartitioningByEnd(seq_len(x2_cumlen))
aranges1
## Then we use it to fragment 'x2':
extractListFragments(x2, aranges1)
extractListFragments(x2b, aranges1)
extractListFragments(x2c, aranges1, use.mcols=TRUE)
## === D2. Fragment a Partitioning object ===
partitioning2 <- PartitioningByEnd(x2b) # same as PartitioningByEnd(x2)
extractListFragments(partitioning2, aranges2)
## Note that when the 1st arg is a Partitioning derivative, then
## swapping the 1st and 2nd elements in the call to extractListFragments()
## doesn't change the returned partitioning:
extractListFragments(aranges2, partitioning2)
## ---------------------------------------------------------------------
## D. SANITY CHECKS
## ---------------------------------------------------------------------
## If 'aranges' is 'PartitioningByEnd(x)' or 'PartitioningByWidth(x)'
## and 'x' has no zero-length list elements, then
## 'extractListFragments(x, aranges, use.mcols=TRUE)' is a no-op.
check_no_ops <- function(x) {
aranges <- PartitioningByEnd(x)
stopifnot(identical(
extractListFragments(x, aranges, use.mcols=TRUE), x
))
aranges <- PartitioningByWidth(x)
stopifnot(identical(
extractListFragments(x, aranges, use.mcols=TRUE), x
))
}
check_no_ops(x2[lengths(x2) != 0])
check_no_ops(x2b[lengths(x2b) != 0])
check_no_ops(x2c[lengths(x2c) != 0])
check_no_ops(gr)
|
Example output
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':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
IntegerList of length 2
[["a"]] 101 102 103 104 105 106 107 108 109
[["b"]] 5 4 3 2 1 0 -1 -2 -3 -4 -5
IRanges object with 5 ranges and 0 metadata columns:
start end width
<integer> <integer> <integer>
[1] 2 3 2
[2] 4 6 3
[3] 8 14 7
[4] 17 16 0
[5] 17 19 3
IntegerList of length 6
[["a"]] 102 103
[["a"]] 104 105 106
[["a"]] 108 109
[["b"]] 5 4 3 2 1
[["b"]] integer(0)
[["b"]] -2 -3 -4
IRanges object with 4 ranges and 1 metadata column:
start end width | label
<integer> <integer> <integer> | <character>
a 1 10 10 | A
b 101 105 5 | B
c 1001 1000 0 | C
d 10001 10012 12 | D
IRanges object with 3 ranges and 2 metadata columns:
start end width | revmap revmap2
<integer> <integer> <integer> | <integer> <integer>
b 103 105 3 | 2 1
c 1001 1000 0 | 3 1
d 10001 10005 5 | 4 1
IRanges object with 3 ranges and 1 metadata column:
start end width | label
<integer> <integer> <integer> | <character>
b 103 105 3 | B
c 1001 1000 0 | C
d 10001 10005 5 | D
IRanges object with 8 ranges and 2 metadata columns:
start end width | revmap revmap2
<integer> <integer> <integer> | <integer> <integer>
a 1 3 3 | 1 1
a 4 10 7 | 1 2
b 101 102 2 | 2 2
b 103 105 3 | 2 3
c 1001 1000 0 | 3 3
d 10001 10010 10 | 4 3
d 10011 10010 0 | 4 4
d 10011 10012 2 | 4 5
IRanges object with 8 ranges and 1 metadata column:
start end width | label
<integer> <integer> <integer> | <character>
a 1 3 3 | A
a 4 10 7 | A
b 101 102 2 | B
b 103 105 3 | B
c 1001 1000 0 | C
d 10001 10010 10 | D
d 10011 10010 0 | D
d 10011 10012 2 | D
IntegerList of length 8
[["a"]] 1 2 3
[["a"]] 4 5 6 7 8 9 10
[["b"]] 101 102
[["b"]] 103 104 105
[["c"]] integer(0)
[["d"]] 10001 10002 10003 10004 10005 10006 10007 10008 10009 10010
[["d"]] integer(0)
[["d"]] 10011 10012
$a
[1] 1 2 3
$a
[1] 4 5 6 7 8 9 10
$b
[1] 101 102
$b
[1] 103 104 105
$c
integer(0)
$d
[1] 10001 10002 10003 10004 10005 10006 10007 10008 10009 10010
$d
integer(0)
$d
[1] 10011 10012
IRangesList of length 2
[[1]]
IRanges object with 2 ranges and 1 metadata column:
start end width | revmap
<integer> <integer> <integer> | <integer>
a 1 10 10 | 1
b 101 103 3 | 2
[[2]]
IRanges object with 3 ranges and 1 metadata column:
start end width | revmap
<integer> <integer> <integer> | <integer>
b 104 105 2 | 2
c 1001 1000 0 | 3
d 10001 10012 12 | 4
IRangesList of length 2
[[1]]
IRanges object with 2 ranges and 1 metadata column:
start end width | label
<integer> <integer> <integer> | <character>
a 1 10 10 | A
b 101 103 3 | B
[[2]]
IRanges object with 3 ranges and 1 metadata column:
start end width | label
<integer> <integer> <integer> | <character>
b 104 105 2 | B
c 1001 1000 0 | C
d 10001 10012 12 | D
IRangesList of length 6
[[1]]
IRanges object with 1 range and 1 metadata column:
start end width | revmap
<integer> <integer> <integer> | <integer>
a 1 5 5 | 1
[[2]]
IRanges object with 1 range and 1 metadata column:
start end width | revmap
<integer> <integer> <integer> | <integer>
a 6 10 5 | 1
[[3]]
IRanges object with 1 range and 1 metadata column:
start end width | revmap
<integer> <integer> <integer> | <integer>
b 101 105 5 | 2
...
<3 more elements>
Loading required package: GenomeInfoDb
GRangesList object of length 2:
[[1]]
GRanges object with 2 ranges and 1 metadata column:
seqnames ranges strand | revmap
<Rle> <IRanges> <Rle> | <integer>
[1] chr1 1-100 * | 1
[2] chr2 1-49950 * | 2
[[2]]
GRanges object with 1 range and 1 metadata column:
seqnames ranges strand | revmap
[1] chr2 49951-100000 * | 2
-------
seqinfo: 2 sequences from an unspecified genome; no seqlengths
GRangesList object of length 1000:
[[1]]
GRanges object with 1 range and 1 metadata column:
seqnames ranges strand | revmap
<Rle> <IRanges> <Rle> | <integer>
[1] chr1 1-100 * | 1
[[2]]
GRanges object with 1 range and 1 metadata column:
seqnames ranges strand | revmap
[1] chr2 1-100 * | 2
[[3]]
GRanges object with 1 range and 1 metadata column:
seqnames ranges strand | revmap
[1] chr2 101-200 * | 2
...
<997 more elements>
-------
seqinfo: 2 sequences from an unspecified genome; no seqlengths
PartitioningByEnd object with 27 ranges and 0 metadata columns:
start end width
<integer> <integer> <integer>
[1] 1 1 1
[2] 2 2 1
[3] 3 3 1
[4] 4 4 1
[5] 5 5 1
... ... ... ...
[23] 23 23 1
[24] 24 24 1
[25] 25 25 1
[26] 26 26 1
[27] 27 27 1
IRanges object with 27 ranges and 2 metadata columns:
start end width | revmap revmap2
<integer> <integer> <integer> | <integer> <integer>
a 1 1 1 | 1 1
a 2 2 1 | 1 2
a 3 3 1 | 1 3
a 4 4 1 | 1 4
a 5 5 1 | 1 5
. ... ... ... . ... ...
d 10008 10008 1 | 4 23
d 10009 10009 1 | 4 24
d 10010 10010 1 | 4 25
d 10011 10011 1 | 4 26
d 10012 10012 1 | 4 27
IntegerList of length 27
[["a"]] 1
[["a"]] 2
[["a"]] 3
[["a"]] 4
[["a"]] 5
[["a"]] 6
[["a"]] 7
[["a"]] 8
[["a"]] 9
[["a"]] 10
...
<17 more elements>
$a
[1] 1
$a
[1] 2
$a
[1] 3
$a
[1] 4
$a
[1] 5
$a
[1] 6
$a
[1] 7
$a
[1] 8
$a
[1] 9
$a
[1] 10
$b
[1] 101
$b
[1] 102
$b
[1] 103
$b
[1] 104
$b
[1] 105
$d
[1] 10001
$d
[1] 10002
$d
[1] 10003
$d
[1] 10004
$d
[1] 10005
$d
[1] 10006
$d
[1] 10007
$d
[1] 10008
$d
[1] 10009
$d
[1] 10010
$d
[1] 10011
$d
[1] 10012
PartitioningByEnd object with 8 ranges and 2 metadata columns:
start end width | revmap revmap2
<integer> <integer> <integer> | <integer> <integer>
a 1 3 3 | 1 1
a 4 10 7 | 1 2
b 11 12 2 | 2 2
b 13 15 3 | 2 3
c 16 15 0 | 3 3
d 16 25 10 | 4 3
d 26 25 0 | 4 4
d 26 27 2 | 4 5
PartitioningByWidth object with 8 ranges and 2 metadata columns:
start end width | revmap revmap2
<integer> <integer> <integer> | <integer> <integer>
[1] 1 3 3 | 1 1
[2] 4 10 7 | 2 1
[3] 11 12 2 | 2 2
[4] 13 15 3 | 3 2
[5] 16 15 0 | 3 3
[6] 16 25 10 | 3 4
[7] 26 25 0 | 4 4
[8] 26 27 2 | 5 4
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