GRangesList-class {GenomicRanges} | R Documentation |
The GRangesList class is a container for storing a collection of GRanges objects. It is derived from GenomicRangesList.
GRangesList(...)
:
Creates a GRangesList object using GRanges objects
supplied in ...
.
makeGRangesListFromFeatureFragments(seqnames=Rle(factor()),
fragmentStarts=list(), fragmentEnds=list(), fragmentWidths=list(),
strand=character(0), sep=",")
:
Constructs a GRangesList object from a list of fragmented features.
See the Examples section below.
In the code snippets below, x
is a GRangesList 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 metadata columns (accessed with
mcols(unlist(x))
).
as.list(x, use.names = TRUE)
:
Creates a list containing the elements of x
.
as(x, "IRangesList")
:
Turns x
into an IRangesList object.
as(from, "GRangesList")
:
Creates a GRangesList object from a RangedDataList
object.
In the following code snippets, x
is a GRanges object.
seqnames(x)
, seqnames(x) <- value
:
Get or set the sequence names in the form of an RleList. value
can be an RleList or CharacterList.
ranges(x)
, ranges(x) <- value
:
Get or set the ranges in the form of a CompressedIRangesList.
value
can be a RangesList object.
strand(x)
, strand(x) <- value
:
Get or set the strand in the form of an RleList. value
can be
an RleList or CharacterList object.
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 GRangesList
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.
seqnameStyle(x)
:
Get or set the seqname style for x
.
Note that this information is not stored in x
but inferred
by looking up seqnames(x)
against a seqname style database
stored in the seqnames.db metadata package (required).
seqnameStyle(x)
is equivalent to seqnameStyle(seqinfo(x))
and can return more than 1 seqname style (with a warning)
in case the style cannot be determined unambiguously.
score(x)
: Get the “score” column from the element
metadata, if any.
In the following code snippets, x
is a GRangesList object.
length(x)
:
Get the number of elements.
names(x)
, names(x) <- value
:
Get or set the names of the elements.
elementLengths(x)
:
Get 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
:
Get or set start(ranges(x))
.
end(x)
, end(x) <- value
:
Get or set end(ranges(x))
.
width(x)
, width(x) <- value
:
Get or set 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.
isDisjoint(x)
Return a vector of logical values indicating
whether the ranges of each element of x
are disjoint
(i.e. non-overlapping).
disjoin(x, ...)
Returns an object of the same type as
x
containing disjoint ranges calculated on each element of
x
.
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
:
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
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:
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
Non-negative integer. The desired length of the output vector.
each
Non-negative integer. Each element of x
is
repeated each
times.
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
, width
The start, end, or width of the window. Two of the three are required.
frequency
, delta
Optional arguments that specify the sampling frequency and increment within the window.
In general, this is more efficient than using "["
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.
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 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.
The methods in this section are isomorphisms, that is, they are endomorphisms
(i.e. they preserve the class of x
) who also preserve the length &
names & metadata columns of x
. In addition, the seqinfo is preserved
too.
range(x)
:
Applies range
to each element in x
.
More precisely, it is equivalent to endoapply(x, range)
.
reduce(x, drop.empty.ranges=FALSE, min.gapwidth=1L)
:
Applies reduce
to each element in x
.
More precisely, it is equivalent to
endoapply(x, reduce, drop.empty.ranges=drop.empty.ranges,
min.gapwidth=min.gapwidth)
.
restrict(x, start = NA, end = NA, keep.all.ranges = FALSE,
use.names = TRUE)
:
Applies restrict
to each element in x
.
flank(x, width, start = TRUE, end = NA, keep.all.ranges = FALSE,
use.names = TRUE, ignore.strand = FALSE)
:
Applies flank
to each element in x
.
P. Aboyoun & H. Pages
GRanges-class,
seqinfo
,
Vector-class,
RangesList-class,
RleList-class,
DataFrameList-class,
coverage-methods,
setops-methods,
findOverlaps-methods
## Construction with 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)) ## Extracting subsets: grl[seqnames(grl) == "chr1", ] grl[seqnames(grl) == "chr1" & strand(grl) == "+", ] ## Renaming the underlying sequences: seqlevels(grl) seqlevels(grl) <- sub("chr", "Chrom", seqlevels(grl)) grl ## range() and reduce(): range(grl) 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. restrict(grl, start=3) ### flank flank(grl, width =20) ## Coerce to IRangesList (seqnames and strand information is lost): as(grl, "IRangesList") ## isDisjoint(): isDisjoint(grl) ## disjoin(): disjoin(grl) # metadata columns and order NOT preserved ## Construction with makeGRangesListFromFeatureFragments(): filepath <- system.file("extdata", "feature_frags.txt", package="GenomicRanges") featfrags <- read.table(filepath, header=TRUE, stringsAsFactors=FALSE) grl2 <- with(featfrags, makeGRangesListFromFeatureFragments(seqnames=targetName, fragmentStarts=targetStart, fragmentWidths=blockSizes, strand=strand)) names(grl2) <- featfrags$RefSeqID grl2