coverage {IRanges} | R Documentation |
Coverage across a set of ranges
Description
Counts the number of times a position is represented in a set of ranges.
Usage
coverage(x, shift=0L, width=NULL, weight=1L, ...)
## S4 method for signature 'RangesList'
coverage(x,
shift = structure(rep(list(0L), length(x)), names = names(x)),
width = structure(rep(list(NULL), length(x)), names = names(x)),
weight = structure(rep(list(1L), length(x)), names = names(x)),
method = c("sort", "hash"))
Arguments
x |
An IRanges, Views, MaskCollection,
RangesList, RangedData object, or any object for which a
coverage method is defined.
|
shift |
For most methods, an integer vector (recycled to the length of
x ) specifying how each element in x should be
(horizontally) shifted before the coverage is computed. Only shifted
indices in the range [1, width ] will be included in the coverage
calculation.
For RangesList and RangedData objects, a list or vector
of the same length as x to be used for the corresponding element
in x . In addition for RangedData objects, can also be
a character vector of length 1 denoting the column to use in
values(x) .
|
width |
For most methods, the length of the returned coverage vector. For
RangesList and RangedData objects, a list or vector of
the same length as x to be used for the corresponding element
in x . In addition for RangedData objects, can also be
a character vector of length 1 denoting the column to use in
values(x) .
If width=NULL (the default), then the specific coverage
method that is actually selected will choose the length of the returned
vector "in a way that makes sense".
For example, when width=NULL , the method for IRanges objects
returns a vector that has just enough elements to have its last
element aligned with the rightmost end of all the ranges in x after
those ranges have been shifted (see the shift argument above).
This ensures that any longer coverage vector would be a "padded with zeros"
version of the vector returned when width=NULL .
When width=NULL , the method for Views objects
returns a vector with length(subject(x)) elements.
When width=NULL , the method for MaskCollection objects
returns a vector with width(x) elements.
|
weight |
For most methods, an integer vector specifying how much each element
in x counts. For RangesList and RangedData
objects, a list or vector of the same length as x to be used
for the corresponding element in x .
For IRanges, Views, MaskCollection and
RangedData objects, this can also be a single string naming
a column in elementMetadata(x) (or in x for
RangedData) to be used as the weights.
|
method |
Settings method to hash is intended only for large
x objects. If method is set to the sort
default, then x is sorted during the calculation of the
coverage Rle. If method is set to hash , then
x is hashed to a vector of size width . Note that
setting method to hash saves time on large x
vectors, but at the expense of additional memory usage.
|
... |
Further arguments to be passed to or from other methods.
|
Value
For most methods, an Rle object representing the coverage of
x
. For RangesList and RangedData objects, a
SimpleRleList object representing a list of coverage vectors.
An integer value called the "coverage" can be associated to each position
in x
, indicating how many times this position is covered by the
elements contained in x
.
For example, if x
is a Views object, the coverage of
a given position in subject(x)
is the number of views it belongs to.
Author(s)
H. Pages and P. Aboyoun
See Also
IRanges-class,
Views-class,
Rle-class,
MaskCollection-class
Examples
x <- IRanges(start=c(-2L, 6L, 9L, -4L, 1L, 0L, -6L, 10L),
width=c( 5L, 0L, 6L, 1L, 4L, 3L, 2L, 3L))
coverage(x)
coverage(x, shift=7)
coverage(x, shift=7, width=27)
coverage(restrict(x, 1, 10))
coverage(reduce(x), shift=7)
coverage(gaps(shift(x, 7), start=1, end=27))
mask1 <- Mask(mask.width=29, start=c(11, 25, 28), width=c(5, 2, 2))
mask2 <- Mask(mask.width=29, start=c(3, 10, 27), width=c(5, 8, 1))
mask3 <- Mask(mask.width=29, start=c(7, 12), width=c(2, 4))
mymasks <- append(append(mask1, mask2), mask3)
coverage(mymasks)
[Package
IRanges version 1.14.4
Index]