IntegerRangesList-class: IntegerRangesList objects
In IRanges: Foundation of integer range manipulation in Bioconductor
Description
Details
Accessors
Coercion
Arithmetic Operations
Author(s)
See Also
Examples
Description
The IntegerRangesList virtual class is a general container for
storing a list of IntegerRanges objects.
Most users are probably more interested in the IRangesList
container, an IntegerRangesList derivative for storing a list of
IRanges objects.
Details
The place of IntegerRangesList in the Vector class hierarchy:
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
Vector
^
|
List
^
|
RangesList
^ ^
/ \
/ \
/ \
/ \
/ \
/ \
IntegerRangesList GenomicRangesList
^ ^
| |
IRangesList GRangesList
^ ^ ^ ^
/ \ / \
/ \ / \
/ \ / \
SimpleIRangesList \ SimpleGRangesList \
CompressedIRangesList CompressedGRangesList
Note that the Vector class hierarchy has many more classes.
In particular Vector, List,
RangesList, and IntegerRangesList
have other subclasses not shown here.
Accessors
In the code snippets below, x is a IntegerRangesList
object.
All of these accessors collapse over the spaces:
start(x), start(x) <- value: Get or set the starts of the
ranges. When setting the starts, value can be an integer vector
of length sum(elementNROWS(x)) or an IntegerList object of
length length(x) and names names(x).
end(x), end(x) <- value: Get or set the ends of the
ranges. When setting the ends, value can be an integer vector
of length sum(elementNROWS(x)) or an IntegerList object of
length length(x) and names names(x).
width(x), width(x) <- value: Get or set the widths of the
ranges. When setting the widths, value can be an integer vector
of length sum(elementNROWS(x)) or an IntegerList object of
length length(x) and names names(x).
space(x): Gets the spaces of the ranges as a
character vector. This is equivalent to names(x), except each
name is repeated according to the length of its element.
Coercion
In the code snippet below, x is an IntegerRangesList object.
-
as.data.frame(x, row.names = NULL, optional = FALSE,
..., value.name = "value", use.outer.mcols = FALSE,
group_name.as.factor = FALSE):
Coerces x to a data.frame. See as.data.frame on the
List man page for details (?List).
In the following code snippet, from is something other than a
IntegerRangesList:
-
as(from, "IntegerRangesList"): When from is a
IntegerRanges, analogous to as.list on a vector.
Arithmetic Operations
Any arithmetic operation, such as x + y, x * y, etc,
where x is a IntegerRangesList, is performed identically on
each element. Currently, IntegerRanges supports only the *
operator, which zooms the ranges by a numeric factor.
Author(s)
M. Lawrence & H. Pagès
See Also
-
IRangesList objects.
-
IntegerRanges and IRanges objects.
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
## ---------------------------------------------------------------------
## Basic manipulation
## ---------------------------------------------------------------------
range1 <- IRanges(start=c(1, 2, 3), end=c(5, 2, 8))
range2 <- IRanges(start=c(15, 45, 20, 1), end=c(15, 100, 80, 5))
named <- IRangesList(one = range1, two = range2)
length(named) # 2
start(named) # same as start(c(range1, range2))
names(named) # "one" and "two"
named[[1]] # range1
unnamed <- IRangesList(range1, range2)
names(unnamed) # NULL
# edit the width of the ranges in the list
edited <- named
width(edited) <- rep(c(3,2), elementNROWS(named))
edited
# same as list(range1, range2)
as.list(IRangesList(range1, range2))
# coerce to data.frame
as.data.frame(named)
IRangesList(range1, range2)
## zoom in 2X
collection <- IRangesList(one = range1, range2)
collection * 2
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
[1] 2
IntegerList of length 2
[["one"]] 1 2 3
[["two"]] 15 45 20 1
[1] "one" "two"
IRanges object with 3 ranges and 0 metadata columns:
start end width
<integer> <integer> <integer>
[1] 1 5 5
[2] 2 2 1
[3] 3 8 6
NULL
IRangesList of length 2
$one
IRanges object with 3 ranges and 0 metadata columns:
start end width
<integer> <integer> <integer>
[1] 1 3 3
[2] 2 4 3
[3] 3 5 3
$two
IRanges object with 4 ranges and 0 metadata columns:
start end width
<integer> <integer> <integer>
[1] 15 16 2
[2] 45 46 2
[3] 20 21 2
[4] 1 2 2
[[1]]
IRanges object with 3 ranges and 0 metadata columns:
start end width
<integer> <integer> <integer>
[1] 1 5 5
[2] 2 2 1
[3] 3 8 6
[[2]]
IRanges object with 4 ranges and 0 metadata columns:
start end width
<integer> <integer> <integer>
[1] 15 15 1
[2] 45 100 56
[3] 20 80 61
[4] 1 5 5
group group_name start end width
1 1 one 1 5 5
2 1 one 2 2 1
3 1 one 3 8 6
4 2 two 15 15 1
5 2 two 45 100 56
6 2 two 20 80 61
7 2 two 1 5 5
IRangesList of length 2
[[1]]
IRanges object with 3 ranges and 0 metadata columns:
start end width
<integer> <integer> <integer>
[1] 1 5 5
[2] 2 2 1
[3] 3 8 6
[[2]]
IRanges object with 4 ranges and 0 metadata columns:
start end width
<integer> <integer> <integer>
[1] 15 15 1
[2] 45 100 56
[3] 20 80 61
[4] 1 5 5
IRangesList of length 2
$one
IRanges object with 3 ranges and 0 metadata columns:
start end width
<integer> <integer> <integer>
[1] 2 3 2
[2] 2 1 0
[3] 4 6 3
[[2]]
IRanges object with 4 ranges and 0 metadata columns:
start end width
<integer> <integer> <integer>
[1] 15 14 0
[2] 59 86 28
[3] 35 64 30
[4] 2 3 2
IRanges documentation built on Dec. 14, 2020, 2 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Description Details Accessors Coercion Arithmetic Operations Author(s) See Also Examples
Description
The IntegerRangesList virtual class is a general container for storing a list of IntegerRanges objects.
Most users are probably more interested in the IRangesList container, an IntegerRangesList derivative for storing a list of IRanges objects.
Details
The place of IntegerRangesList in the Vector class hierarchy:
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 | Vector
^
|
List
^
|
RangesList
^ ^
/ \
/ \
/ \
/ \
/ \
/ \
IntegerRangesList GenomicRangesList
^ ^
| |
IRangesList GRangesList
^ ^ ^ ^
/ \ / \
/ \ / \
/ \ / \
SimpleIRangesList \ SimpleGRangesList \
CompressedIRangesList CompressedGRangesList
|
Note that the Vector class hierarchy has many more classes. In particular Vector, List, RangesList, and IntegerRangesList have other subclasses not shown here.
Accessors
In the code snippets below, x is a IntegerRangesList
object.
All of these accessors collapse over the spaces:
start(x), start(x) <- value: Get or set the starts of the ranges. When setting the starts,valuecan be an integer vector of lengthsum(elementNROWS(x))or an IntegerList object of lengthlength(x)and namesnames(x).end(x), end(x) <- value: Get or set the ends of the ranges. When setting the ends,valuecan be an integer vector of lengthsum(elementNROWS(x))or an IntegerList object of lengthlength(x)and namesnames(x).width(x), width(x) <- value: Get or set the widths of the ranges. When setting the widths,valuecan be an integer vector of lengthsum(elementNROWS(x))or an IntegerList object of lengthlength(x)and namesnames(x).space(x): Gets the spaces of the ranges as a character vector. This is equivalent tonames(x), except each name is repeated according to the length of its element.
Coercion
In the code snippet below, x is an IntegerRangesList object.
-
as.data.frame(x, row.names = NULL, optional = FALSE, ..., value.name = "value", use.outer.mcols = FALSE, group_name.as.factor = FALSE): Coercesxto adata.frame. See as.data.frame on theListman page for details (?List).
In the following code snippet, from is something other than a
IntegerRangesList:
-
as(from, "IntegerRangesList"): Whenfromis aIntegerRanges, analogous toas.liston a vector.
Arithmetic Operations
Any arithmetic operation, such as x + y, x * y, etc,
where x is a IntegerRangesList, is performed identically on
each element. Currently, IntegerRanges supports only the *
operator, which zooms the ranges by a numeric factor.
Author(s)
M. Lawrence & H. Pagès
See Also
-
IRangesList objects.
-
IntegerRanges and IRanges objects.
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 | ## ---------------------------------------------------------------------
## Basic manipulation
## ---------------------------------------------------------------------
range1 <- IRanges(start=c(1, 2, 3), end=c(5, 2, 8))
range2 <- IRanges(start=c(15, 45, 20, 1), end=c(15, 100, 80, 5))
named <- IRangesList(one = range1, two = range2)
length(named) # 2
start(named) # same as start(c(range1, range2))
names(named) # "one" and "two"
named[[1]] # range1
unnamed <- IRangesList(range1, range2)
names(unnamed) # NULL
# edit the width of the ranges in the list
edited <- named
width(edited) <- rep(c(3,2), elementNROWS(named))
edited
# same as list(range1, range2)
as.list(IRangesList(range1, range2))
# coerce to data.frame
as.data.frame(named)
IRangesList(range1, range2)
## zoom in 2X
collection <- IRangesList(one = range1, range2)
collection * 2
|
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
[1] 2
IntegerList of length 2
[["one"]] 1 2 3
[["two"]] 15 45 20 1
[1] "one" "two"
IRanges object with 3 ranges and 0 metadata columns:
start end width
<integer> <integer> <integer>
[1] 1 5 5
[2] 2 2 1
[3] 3 8 6
NULL
IRangesList of length 2
$one
IRanges object with 3 ranges and 0 metadata columns:
start end width
<integer> <integer> <integer>
[1] 1 3 3
[2] 2 4 3
[3] 3 5 3
$two
IRanges object with 4 ranges and 0 metadata columns:
start end width
<integer> <integer> <integer>
[1] 15 16 2
[2] 45 46 2
[3] 20 21 2
[4] 1 2 2
[[1]]
IRanges object with 3 ranges and 0 metadata columns:
start end width
<integer> <integer> <integer>
[1] 1 5 5
[2] 2 2 1
[3] 3 8 6
[[2]]
IRanges object with 4 ranges and 0 metadata columns:
start end width
<integer> <integer> <integer>
[1] 15 15 1
[2] 45 100 56
[3] 20 80 61
[4] 1 5 5
group group_name start end width
1 1 one 1 5 5
2 1 one 2 2 1
3 1 one 3 8 6
4 2 two 15 15 1
5 2 two 45 100 56
6 2 two 20 80 61
7 2 two 1 5 5
IRangesList of length 2
[[1]]
IRanges object with 3 ranges and 0 metadata columns:
start end width
<integer> <integer> <integer>
[1] 1 5 5
[2] 2 2 1
[3] 3 8 6
[[2]]
IRanges object with 4 ranges and 0 metadata columns:
start end width
<integer> <integer> <integer>
[1] 15 15 1
[2] 45 100 56
[3] 20 80 61
[4] 1 5 5
IRangesList of length 2
$one
IRanges object with 3 ranges and 0 metadata columns:
start end width
<integer> <integer> <integer>
[1] 2 3 2
[2] 2 1 0
[3] 4 6 3
[[2]]
IRanges object with 4 ranges and 0 metadata columns:
start end width
<integer> <integer> <integer>
[1] 15 14 0
[2] 59 86 28
[3] 35 64 30
[4] 2 3 2
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.