| GRangesList-class {GenomicRanges} | R Documentation |
The GRangesList class is a container for storing a collection of GRanges objects.
GRangesList(...):
Creates a GRangesList object using GRanges objects
supplied in ....
In the code snippets below, x is a GRangesList object.
as(from, "GRangesList"):
Creates a GRangesList object from a RangedDataList object.
as.data.frame(x, row.names = NULL, optional = FALSE):
Creates a data.frame with columns element (character),
seqnames (factor), start (integer),
end (integer), width (integer), strand (factor),
as well as the additional columns stored in
elementMetadata(unlist(x)).
as.list(x, use.names = TRUE):
Creates a list containing the elements of x.
In the following code snippets, x is a GRanges object.
seqnames(x), seqnames(x) <- value:
Gets or sets the sequence names in the form of an RleList. value
can be an RleList or CharacterList.
ranges(x), ranges(x) <- value:
Gets or sets the ranges in the form of a CompressedIRangesList.
value can be a RangesList object.
strand(x), strand(x) <- value:
Gets or sets the strand in the form of an RleList. value can be
an RleList or CharacterList object.
seqinfo(x):
Returns a Seqinfo object containing information about
the underlying sequences.
seqlengths(x), seqlengths(x) <- value:
Gets or sets the seqlengths. seqlengths(x) is formally
equivalent to seqlengths(seqinfo(x)).
value can be a named non-negative integer or numeric vector.
isCircular(x):
Formally equivalent to isCircular(seqinfo(x)).
isCircularWithKnownLength(x):
Formally equivalent to isCircularWithKnownLength(seqinfo(x)).
elementMetadata(x), elementMetadata(x) <- value:
Gets or sets the optional data columns for the GRangesList elements.
value can be a DataFrame, data.frame object, or NULL.
values(x), values(x) <- value:
Alternative to elementMetadata functions.
In the following code snippets, x is a GRangesList object.
length(x):
Gets the number of elements.
names(x), names(x) <- value:
Gets or sets the names of the elements.
elementLengths(x):
Gets the length of each of the elements.
isEmpty(x):
Returns a logical indicating either if the GRangesList has no
elements or if all its elements are empty.
In the following code snippets, x is a GRangesList object.
start(x), start(x) <- value:
Gets or sets start(ranges(x)).
end(x), end(x) <- value:
Gets or sets end(ranges(x)).
width(x), width(x) <- value:
Gets or sets width(ranges(x)).
shift(x, shift, use.names=TRUE):
Returns a new GRangesList object containing intervals with start and
end values that have been shifted by integer vector shift.
The use.names argument determines whether or not to
keep the names on the ranges.
coverage(x, shift = list(0L), width = list(NULL), weight = list(1L)):
Returns a named RleList object with one element
('integer' Rle) per unique sequence name representing how many
times each position in the sequence is covered by the intervals in
x. The shift, width, and weight arguments
take list arguments, possibly named by the unique sequence names in
x, whose elements are passed into the coverage method for
IRanges object. See ?coverage for more
information on these optional arguments.
In the code snippets below, x is a GRangesList object.
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.
c(x, ...):
Combines x and the GRangesList 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.
unlist(x, recursive = TRUE, use.names = TRUE):
Concatenates the elements of x into a single GRanges
object.
In the following code snippets, x is a GRangesList object.
x[i, j], x[i, j] <- value:
Gets or sets elements i with optional values columns
values(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:
Gets or sets element i, where i is a numeric or character
vector of length 1.
x$name, x$name <- value:
Gets or sets 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
GRangesList object.
If n is negative, returns all but the last abs(n) elements
of the GRangesList object.
rep(x, times, length.out, each):
Repeats the values in x through one of the following conventions:
timeslength(x), or to repeat the whole vector
if of length 1.length.outeachx is
repeated each times.rev(x):
Returns a new object of the same class as x made of the original
elements in the reverse order.
seqselect(x, start=NULL, end=NULL, width=NULL):
Similar to window, except that multiple consecutive subsequences
can be requested for concatenation. As such two of the three start,
end, and width arguments can be used to specify the
consecutive subsequences. Alternatively, start can take a Ranges
object or something that can be converted to a Ranges object like an
integer vector, logical vector or logical Rle. If the concatenation of
the consecutive subsequences is undesirable, consider using
Views.
seqselect(x, start=NULL, end=NULL, width=NULL) <- value:
Similar to window<-, except that multiple consecutive subsequences
can be replaced by a value whose length is a divisor of the number
of elements it is replacing. As such two of the three start,
end, and width arguments can be used to specify the
consecutive subsequences. Alternatively, start can take a Ranges
object or something that can be converted to a Ranges object like an
integer vector, logical vector or logical Rle.
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
GRanges object.
If n is negative, returns all but the first abs(n) elements
of the GRanges object.
window(x, start = NA, end = NA, width = NA, frequency = NULL, delta = NULL, ...):
Extracts the subsequence window from the GRanges object using:
start, end, widthfrequency, delta"[" operator.
window(x, start = NA, end = NA, width = NA, keepLength = TRUE) <- value:
Replaces the subsequence window specified on the left (i.e. the subsequence
in x specified by start, end and width)
by value.
value must either be of class class(x), belong to a subclass
of class(x), be coercible to class(x), or be NULL.
If keepLength is TRUE, the elements of value are
repeated to create a GRanges object with the same number of elements
as the width of the subsequence window it is replacing.
If keepLength is FALSE, this replacement method can modify
the length of x, depending on how the length of the left
subsequence window compares to the length of value.
In the code snippets below, x is a GRangesList 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 GRangesList 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
GRangesList objects.
mapply(FUN, ..., MoreArgs = NULL, SIMPLIFY = TRUE, USE.NAMES = TRUE):
Like the standard mapply function defined in the
base package, the mapply method for GRangesList 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 GRangesList objects
is a user-friendly version of lapply by default returning a vector
or matrix if appropriate.
In the code snippets below, x is a GRangesList object.
reduce(x, drop.empty.ranges=FALSE, min.gapwidth=1L):
Reduces separately each element in x and returns them in a
GRangesList object with the same length & names & elementMetadata &
seqinfo as x. In other words, it is equivalent to
endoapply(x, reduce, drop.empty.ranges=drop.empty.ranges,
min.gapwidth=min.gapwidth).
P. Aboyoun
GRanges-class, Seqinfo-class Sequence-class, RangesList-class, RleList-class, DataFrameList-class
## Construction using GRangesList
gr1 <-
GRanges(seqnames = "chr2", ranges = IRanges(3, 6),
strand = "+", score = 5L, GC = 0.45)
gr2 <-
GRanges(seqnames = c("chr1", "chr1"),
ranges = IRanges(c(7,13), width = 3),
strand = c("+", "-"), score = 3:4, GC = c(0.3, 0.5))
gr3 <-
GRanges(seqnames = c("chr1", "chr2"),
ranges = IRanges(c(1, 4), c(3, 9)),
strand = c("-", "-"), score = c(6L, 2L), GC = c(0.4, 0.1))
grl <- GRangesList("gr1" = gr1, "gr2" = gr2, "gr3" = gr3)
grl
# Summarizing elements
elementLengths(grl)
table(seqnames(grl))
coverage(grl)
# Extracting subsets
grl[seqnames(grl) == "chr1", ]
grl[seqnames(grl) == "chr1" & strand(grl) == "+", ]
# Changing sequence name
unique(seqnames(grl))
seqnames(grl) <- sub("chr", "Chrom", seqnames(grl))
grl
# reduce():
reduce(grl) # Doesn't really reduce anything but note the reordering
# of the inner elements in the 3rd top-level element: the
# ranges are reordered by sequence name first (the order of
# the sequence names is dictated by the sequence levels),
# and then by strand.