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 ...
.
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
RangesList
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.frame-like object (i.e.
DataFrame
or data.frame) holding
element-wise 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 non-negative 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.
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 intra-pair 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 intra-pair distances,
$(pos_{2} - pos_{1}, \ldots, pos_{m} - pos_{m - 1})$.
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
.
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 re-creatable.
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 NA-free
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 non-negative, 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
length(x)
, or to repeat the whole vector
if of length 1.length.out
each
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 non-negative, 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.
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.
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.
x
.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 user-friendly version of lapply
by default returning a vector
or matrix if appropriate.
seqinfo
,
GRangesList-class,
Vector-class,
RangesList-class,
RleList-class,
DataFrameList-class,
findOverlaps-methods
## Construction of GTuplesList of 4-tuples 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 intra-pair 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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