Description Constructors Accessors Coercion Subsetting Combining Looping Author(s) See Also Examples
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 ...
, either consecutively or in a list.
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 following code snippets, x
is a GRanges object.
length(x)
:
Get the number of list elements.
names(x)
, names(x) < value
:
Get or set the names on x
.
elementNROWS(x)
:
Get a vector of the length
of each of the list element.
isEmpty(x)
:
Returns a logical indicating either if the GRangesList 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.
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.
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))
.
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, pruning.mode=c("error", "coarse", "fine", "tidy")) < 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 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 code snippets below, x
is a GRangesList 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, "IRangesList")
:
Turns x
into an IRangesList object.
When x
is a list
of GRanges
, it can be coerced to a
GRangesList
.
as(x, "GRangesList")
:
Turns x
into a GRangesList
.
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 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
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
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
GRanges object.
If n
is negative, returns all but the first abs(n)
elements
of the GRanges object.
In the code snippets below, x
is a GRangesList object.
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
.
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 GRanges
object.
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 userfriendly version of lapply
by default returning a vector
or matrix if appropriate.
P. Aboyoun & H. Pagès
GRangesclass,
seqinfo
,
Vectorclass,
RangesListclass,
RleListclass,
DataFrameListclass,
intrarangemethods,
interrangemethods,
coveragemethods,
setopsmethods,
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 45 46 47 48  ## 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:
elementNROWS(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
## 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

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