GRangesList objects
The GRangesList class is a container for storing a collection of GRanges objects. It is a subclass of GenomicRangesList. It exists in 2 flavors: SimpleGRangesList and CompressedGRangesList. Each flavor uses a particular internal representation. The CompressedGRangesList flavor is the default. It is particularly efficient for storing a large number of list elements and operating on them.
GRangesList(..., compress=TRUE):Creates a GRangesList object using the GRanges objects
supplied in ..., either consecutively or in a list.
By default a CompressedGRangesList instance is returned,
that is, a GRangesList object of the CompressedGRangesList flavor.
Use compress=FALSE to get a SimpleGRangesList instance
instead.
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.
length(x):Get the number of list elements.
names(x), names(x) <- value:Get or set the names on x.
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 an IntegerRangesList 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 object.
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.
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.
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 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.
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 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:
timesVector 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.outNon-negative integer. The desired length of the output vector.
eachNon-negative 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 non-negative, returns the last n list elements of the
GRangesList object.
If n is negative, returns all but the first abs(n)
list elements of the GRangesList 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.
fA binary argument function.
initAn R object of the same kind as the elements of x.
rightA logical indicating whether to proceed from left to right (default) or from right to left.
nomatchThe 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.
P. Aboyoun & H. Pagès
GRanges objects.
seqinfo in the GenomeInfoDb
package.
IntegerRangesList objects in the IRanges package.
RleList objects in the IRanges package.
DataFrameList objects in the IRanges package.
intra-range-methods, inter-range-methods, coverage-methods, setops-methods, and findOverlaps-methods.
GenomicRangesList objects.
## Construction with GRangesList():
gr1 <- GRanges("chr2", IRanges(3, 6),
strand="+", score=5L, GC=0.45)
gr2 <- GRanges(c("chr1", "chr1"), IRanges(c(7,13), width=3),
strand=c("+", "-"), score=3:4, GC=c(0.3, 0.5))
gr3 <- GRanges(c("chr1", "chr2"), 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
grl2Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.