GRanges(seqnames = Rle(), ranges = IRanges(),
strand = Rle("*", length(seqnames)),
...,
seqlengths = NULL, seqinfo = NULL):
Creates a GRanges object.
seqnamesrangesstrand..."start", "end", "width", or
"element". A named integer vector "seqlength"
can be used instead of seqinfo.seqlengthslevel(seqnames).seqinfolevel(seqnames).x is a GRanges object. as(from, "GRanges"): Creates a GRanges object from a
RangedData, RangesList, RleList or RleViewsList object. Coercing a data.frame or DataFrame into a GRanges object is also
supported. See makeGRangesFromDataFrame for the details.
as(from, "RangedData"):
Creates a RangedData object from a GRanges
object. The strand and metadata columns become columns
in the result. The seqlengths(from), isCircular(from),
and genome(from) vectors are stored in the metadata columns
of ranges(rd).
as(from, "RangesList"):
Creates a RangesList object from a GRanges
object. The strand and metadata columns become inner
metadata columns (i.e. metadata columns on the ranges).
The seqlengths(from), isCircular(from), and
genome(from) vectors become the metadata columns.
as.data.frame(x, row.names = NULL, optional = FALSE, ...):
Creates a data.frame with columns seqnames (factor),
start (integer), end (integer), width (integer),
strand (factor), as well as the additional metadata columns
stored in mcols(x). Pass an explicit
stringsAsFactors=TRUE/FALSE argument via ... to
override the default conversions for the metadata columns in
mcols(x).
x is a Seqinfo
object. as(x, "GRanges"), as(x, "GenomicRanges"),
as(x, "RangesList"): Turns Seqinfo object
x (with no NA lengths) into a GRanges or RangesList.
x is a GRanges object. length(x):
Get the number of elements.
seqnames(x), seqnames(x) <- value:
Get or set the sequence names.
value can be an Rle object, a character vector,
or a factor.
ranges(x), ranges(x) <- value:
Get or set the ranges. value can be a Ranges object.
names(x), names(x) <- value:
Get or set the names of the elements.
strand(x), strand(x) <- value:
Get or set the strand. value can be an Rle object, character
vector, or factor.
mcols(x, use.names=FALSE), mcols(x) <- value:
Get or set the metadata columns.
If use.names=TRUE and the metadata columns are not NULL,
then the names of x are propagated as the row names of the
returned DataFrame object.
When setting the metadata columns, the supplied value must be NULL
or a data.frame-like object (i.e. DataTable or data.frame)
object 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 GRanges 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”
column from the element metadata.
granges(x, use.mcols=FALSE): Gets a GRanges with
only the range information from x, unless use.mcols
is TRUE, in which case the metadata columns are also
returned. Those columns will include any "extra column slots" if
x is a specialized GenomicRanges derivative.
x is a GRanges 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)).
x is a GRanges 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 GRanges 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.
c(x, ..., ignore.mcols=FALSE)
If the GRanges objects have metadata columns (represented as one
DataFrame per object), each such DataFrame must have the
same columns in order to combine successfully. In order to circumvent
this restraint, you can pass in an ignore.mcols=TRUE argument
which will combine all the objects into one and drop all of their
metadata columns.
split(x, f, drop=FALSE):
Splits x according to f to create a
GRangesList object.
If f is a list-like object then drop is ignored
and f is treated as if it was
rep(seq_len(length(f)), sapply(f, length)),
so the returned object has the same shape as f (it also
receives the names of f).
Otherwise, if f is not a list-like object, empty list
elements are removed from the returned object if drop is
TRUE.
tile(x, n, width): Splits x into a
GRangesList, each element of which corresponds to a tile,
or partition, of x. Specify the tile geometry with either
n or width (not both). Passing n creates
n tiles of approximately equal width, truncated by sequence
end, while passing width tiles the region with ranges of
the given width, again truncated by sequence end.
x is a GRanges 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; or a 'logical' Rle object.
x[i,j] <- value:
Replaces elements i and optional metadata columns j
with value.
head(x, n = 6L):
If n is non-negative, returns the first n elements of the
GRanges object.
If n is negative, returns all but the last abs(n) elements
of the GRanges 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.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.
x$name, x$name <- value:
Shortcuts for mcols(x)$name and mcols(x)$name <- value,
respectively. Provided as a convenience, for GRanges objects *only*,
and as the result of strong popular demand.
Note that those methods are not consistent with the other $
and $<- methods in the IRanges/GenomicRanges infrastructure,
and might confuse some users by making them believe that a GRanges
object can be manipulated as a data.frame-like object.
Therefore we recommend using them only interactively, and we discourage
their use in scripts or packages. For the latter, use
mcols(x)$name and mcols(x)$name <- value, instead
of x$name and x$name <- value, respectively.
x is a list or List object with
names on it, and the subscript i is a GRanges object with all its
seqnames being valid x names. x[i]:
Return an object of the same class as x and parallel
to i. More precisely, it's conceptually doing:
as(lapply(i, function(ii) x[[seqnames(ii)]][ranges(ii)]), class(x))
show(x):
By default the show method displays 5 head and 5 tail
elements. This can be changed by setting the global options
showHeadLines and showTailLines. If the object
length is less than (or equal to) the sum of these 2 options
plus 1, then the full object is displayed.
Note that these options also affect the display of
GAlignments and
GAlignmentPairs objects (defined in
the GenomicAlignments package), as well as other objects
defined in the IRanges and Biostrings packages (e.g.
IRanges and DNAStringSet objects).
seqnames
ranges
strand
mcols"seqnames", "ranges", "strand",
"seqlevels", "seqlengths", "isCircular",
"start", "end", "width", or "element".
seqinfo
makeGRangesFromDataFrame,
GRangesList-class,
seqinfo,
Vector-class,
Rle-class,
Ranges-class,
DataFrame-class,
intra-range-methods,
inter-range-methods,
setops-methods,
findOverlaps-methods,
nearest-methods,
coverage-methods
seqinfo <- Seqinfo(paste0("chr", 1:3), c(1000, 2000, 1500), NA, "mock1")
gr <-
GRanges(seqnames =
Rle(c("chr1", "chr2", "chr1", "chr3"), c(1, 3, 2, 4)),
ranges = IRanges(
1:10, width = 10:1, names = head(letters,10)),
strand = Rle(
strand(c("-", "+", "*", "+", "-")),
c(1, 2, 2, 3, 2)),
score = 1:10,
GC = seq(1, 0, length=10),
seqinfo=seqinfo)
gr
## Summarizing elements
table(seqnames(gr))
sum(width(gr))
summary(mcols(gr)[,"score"])
## Renaming the underlying sequences
seqlevels(gr)
seqlevels(gr) <- sub("chr", "Chrom", seqlevels(gr))
gr
seqlevels(gr) <- sub("Chrom", "chr", seqlevels(gr)) # revert
## Combining objects
gr2 <- GRanges(seqnames=Rle(c('chr1', 'chr2', 'chr3'), c(3, 3, 4)),
IRanges(1:10, width=5), strand='-',
score=101:110, GC = runif(10),
seqinfo=seqinfo)
gr3 <- GRanges(seqnames=Rle(c('chr1', 'chr2', 'chr3'), c(3, 4, 3)),
IRanges(101:110, width=10), strand='-',
score=21:30,
seqinfo=seqinfo)
some.gr <- c(gr, gr2)
## all.gr <- c(gr, gr2, gr3) ## (This would fail)
all.gr <- c(gr, gr2, gr3, ignore.mcols=TRUE)
## Subsetting a named list-like object *by* a GRanges subscript
x <- RleList(chr1=101:120, chr2=2:-8, chr3=31:40)
x[gr]
## The number of lines displayed in the 'show' method
## are controlled with two global options.
longGR <- c(gr[,"score"], gr2[,"score"], gr3)
longGR
options("showHeadLines"=7)
options("showTailLines"=2)
longGR
## Revert to default values
options("showHeadLines"=NULL)
options("showTailLines"=NULL)
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