Description Constructor Accessors Tuples methods Coercion Subsetting Combining Looping Author(s) See Also Examples
The GTuplesList
class is a container for storing a collection of
GTuples
objects. It is derived from
GRangesList
.
GTuplesList(...)
:
Creates a GTuplesList
object using GTuples
objects
supplied in ...
.
In the following code snippets, x
is a GTuplesList
object.
length(x)
:
Get the number of list elements.
names(x)
, names(x) < value
:
Get or set the names on x
.
elementNROWS(x)
:
Get the length
of each of the list elements.
isEmpty(x)
:
Returns a logical indicating either if the GTuplesList
has no
elements or if all its elements are empty.
seqnames(x)
, seqnames(x) < value
:
Get or set the sequence names in the form of an
RleList
. value
can be an
RleList
or CharacterList
object.
tuples(x)
, tuples(x) < value
:
Get or set the tuples in the form of a
SimpleList
of integer matrices. value
can
be a a single integer matrix.
ranges(x, use.mcols = FALSE)
, ranges(x) < value
: Get or
set the ranges in the form of a
CompressedIRangesList
. value
can be a
IntegerRangesList
object.
WARNING: The use of ranges
with GTuplesList
objects is strongly discouraged. It will only get/set
pos_{1} and pos_{m} of the tuples, where m is the
size
of the tuples, as these are what are stored in the "ranges"
slot of the GTuples
objects.
strand(x)
, strand(x) < value
:
Get or set the strand in the form of an RleList
.
value
can be an RleList
,
CharacterList
or single character. value
as
a single character converts all ranges in x
to the same
value
; for selective strand conversion (i.e., mixed “+”
and “”) use RleList
or
CharacterList
.
mcols(x, use.names=FALSE)
, mcols(x) < value
:
Get or set the metadata columns.
value
can be NULL
, or a data.framelike object (i.e.
DataFrame
or data.frame) holding
elementwise metadata.
elementMetadata(x)
, elementMetadata(x) < value
,
values(x)
, values(x) < value
:
Alternatives to mcols
functions. Their use is discouraged.
seqinfo(x)
, seqinfo(x) < value
:
Get or set the information about the underlying sequences.
value
must be a Seqinfo object.
seqlevels(x)
, seqlevels(x, force=FALSE) < value
:
Get or set the sequence levels.
seqlevels(x)
is equivalent to seqlevels(seqinfo(x))
or to levels(seqnames(x))
, those 2 expressions being
guaranteed to return identical character vectors on a GTuplesList
object. value
must be a character vector with no NAs.
See ?seqlevels
for more information.
seqlengths(x)
, seqlengths(x) < value
:
Get or set the sequence lengths.
seqlengths(x)
is equivalent to seqlengths(seqinfo(x))
.
value
can be a named nonnegative integer or numeric vector
eventually with NAs.
isCircular(x)
, isCircular(x) < value
:
Get or set the circularity flags.
isCircular(x)
is equivalent to isCircular(seqinfo(x))
.
value
must be a named logical vector eventually with NAs.
genome(x)
, genome(x) < value
:
Get or set the genome identifier or assembly name for each sequence.
genome(x)
is equivalent to genome(seqinfo(x))
.
value
must be a named character vector eventually with NAs.
seqlevelsStyle(x)
, seqlevelsStyle(x) < value
:
Get or set the seqname style for x
.
See the seqlevelsStyle generic getter and setter
in the GenomeInfoDb package for more information.
score(x), score(x) < value
: Get or set the “score”
metadata column.
In the following code snippets, x is a GTuplesList
object.
WARNING: The preferred setter is tuples(x) < value
and the
use of start(x) < value
, end(x) < value
and
width(x) < value is discouraged
.
start(x)
, start(x) < value
:
Get or set pos_{1} of the tuples
. WARNING: The use
of start(x) < value
is discouraged; instead, construct the
tuples as the appropriate List
of integer matrices, mvalue
,
and use tuples(x) < mvalue
.
end(x)
, end(x) < value
:
Get or set pos_{m} of the tuples, where m is the size
of the tuples. WARNING: The use of end(x) < value
is
discouraged; instead, construct the tuples as the appropriate List
of integer matrices, mvalue
, and use tuples(x) < mvalue
.
IPD(x)
: Get the intrapair distances (IPD
) in the form of a
SimpleList
of integer matrices. IPD
is
only defined for tuples with size
> 1. The IPD
of a tuple
with size
= m is the vector of intrapair distances,
(pos_{2}  pos_{1}, …, pos_{m}  pos_{m  1}).
width(x)
, width(x) < value
:
Get or set pos_{m}  pos_{1} of the tuples, where m is the
size
of the tuples. If using width(x) < value
,
pos_{1} is held fixed and pos_{m} is altered.
WARNING: The use of width(x) < value
is discouraged;
instead, instead, construct the tuples as the appropriate List
of integer matrices, mvalue
, and use tuples(x) < mvalue
.
In the code snippets below, x
is a GTuplesList 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
).
as.list(x, use.names = TRUE)
:
Creates a list containing the elements of x
.
as(x, "GRangesList")
: Creates a
GRangesList
object from a
GTuplesList
object. WARNING: This is generally a
destructive operation, as the original GTuplesList
may not
be recreatable.
In the following code snippets, x
is a GTuplesList
object.
x[i, j]
, x[i, j] < value
:
Get or set elements i
with optional metadata columns
mcols(x)[,j]
, where i
can be missing; an NAfree
logical, numeric, or character vector; a 'logical' Rle object, or
an AtomicList object.
x[[i]]
, x[[i]] < value
:
Get or set element i
, where i
is a numeric or character
vector of length 1.
x$name
, x$name < value
:
Get or set element name
, where name
is a name or character
vector of length 1.
head(x, n = 6L)
:
If n
is nonnegative, returns the first n elements of the
GTuplesList object.
If n
is negative, returns all but the last abs(n)
elements
of the GTuplesList object.
rep(x, times, length.out, each)
:
Repeats the values in x
through one of the following conventions:
times
Vector giving the number of times to repeat each
element if of length length(x)
, or to repeat the whole vector
if of length 1.
length.out
Nonnegative integer. The desired length of the output vector.
each
Nonnegative integer. Each element of x
is
repeated each
times.
subset(x, subset)
:
Returns a new object of the same class as x
made of the subset
using logical vector subset
, where missing values are taken as
FALSE
.
tail(x, n = 6L)
:
If n
is nonnegative, returns the last n elements of the
GTuples object.
If n
is negative, returns all but the first abs(n)
elements
of the GTuples object.
In the code snippets below, x
is a GTuplesList object.
c(x, ...)
:
Combines x
and the GTuplesList objects in ...
together. Any object in ...
must belong to the same class
as x
, or to one of its subclasses, or must be NULL
.
The result is an object of the same class as x
.
append(x, values, after = length(x))
:
Inserts the values
into x
at the position given by
after
, where x
and values
are of the same
class.
unlist(x, recursive = TRUE, use.names = TRUE)
:
Concatenates the elements of x
into a single GTuples
object.
In the code snippets below, x
is a GTuplesList object.
endoapply(X, FUN, ...)
:
Similar to lapply
, but performs an endomorphism,
i.e. returns an object of class(X)
.
lapply(X, FUN, ...)
:
Like the standard lapply
function defined in the
base package, the lapply
method for GTuplesList objects
returns a list of the same length as X
, with each element being
the result of applying FUN
to the corresponding element of
X
.
Map(f, ...)
:
Applies a function to the corresponding elements of given
GTuplesList objects.
mapply(FUN, ..., MoreArgs = NULL, SIMPLIFY = TRUE,
USE.NAMES = TRUE)
:
Like the standard mapply
function defined in the
base package, the mapply
method for GTuplesList objects is a
multivariate version of sapply
.
mendoapply(FUN, ..., MoreArgs = NULL)
:
Similar to mapply
, but performs an endomorphism
across multiple objects, i.e. returns an object of
class(list(...)[[1]])
.
Reduce(f, x, init, right = FALSE, accumulate = FALSE)
:
Uses a binary function to successively combine the elements of x
and a possibly given initial value.
A binary argument function.
An R object of the same kind as the elements of x
.
A logical indicating whether to proceed from left to right (default) or from right to left.
The value to be returned in the case when "no match" (no element satisfying the predicate) is found.
sapply(X, FUN, ..., simplify=TRUE, USE.NAMES=TRUE)
:
Like the standard sapply
function defined in
the base package, the sapply
method for GTuplesList objects
is a userfriendly version of lapply
by default returning a vector
or matrix if appropriate.
Peter Hickey for GTuplesList
definition and methods. P. Aboyoun
& H. Pagès for all the real work underlying the powerful GRangesList
class and methods.
GTuplesclass
seqinfo
,
GRangesListclass,
Vectorclass,
IntegerRangesListclass,
RleListclass,
DataFrameListclass,
findOverlapsmethods
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  ## Construction of GTuplesList of 4tuples with GTuplesList():
seqinfo < Seqinfo(paste0("chr", 1:3), c(1000, 2000, 1500), NA, "mock1")
gt4 < GTuples(seqnames = Rle(c("chr1", "chr2", "chr1", "chr3"),
c(1, 3, 2, 4)),
tuples = matrix(c(1:10, 2:11, 3:12, 4:13), ncol = 4),
strand = Rle(strand(c("", "+", "*", "+", "")),
c(1, 2, 2, 3, 2)),
score = 1:10, GC = seq(1, 0, length = 10), seqinfo = seqinfo)
gtl4 < GTuplesList(A = gt4[1:4], B = gt4[5:10])
gtl4
## Summarizing elements:
elementNROWS(gtl4)
table(seqnames(gtl4))
## Extracting subsets:
gtl4[seqnames(gtl4) == "chr1", ]
gtl4[seqnames(gtl4) == "chr1" & strand(gtl4) == "+", ]
## Renaming the underlying sequences:
seqlevels(gtl4)
seqlevels(gtl4) < sub("chr", "Chrom", seqlevels(gtl4))
gtl4
## Coerce to GRangesList ("internal positions" information is lost):
as(gtl4, "GRangesList")
## Get the size of the tuples stored in the GTuplesList object
size(gtl4)
## Get the tuples
tuples(gtl4)
## Get the matrix of intrapair distances (IPD)
IPD(gtl4)
## Can't combine genomic tuples of different sizes
gt1 < GTuples('chr1', matrix(30:40))
gt1
## Not run:
## Returns error
GTuplesList(A = gt4, gt1)
## End(Not run)

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