| coverage {IRanges} | R Documentation |
Counts the number of times a position is represented in a set of ranges.
## Old interface (IRanges < 1.1.58): #coverage(x, start=NA, end=NA, ...) ## Transitional interface (the current one): coverage(x, start=NA, end=NA, shift=0L, width=NULL, weight=1L, ...) ## New interface (in the near future): #coverage(x, shift=0L, width=NULL, weight=1L, ...)
x |
An IRanges, Views or MaskCollection object,
or any object for which a coverage method is defined.
|
start, end |
Single integers specifying the position in x where to start
and end the extraction of the coverage.
IMPORTANT NOTE: Please do not use these arguments (use the shift/width
arguments below). They are temporarily kept for backward compatibility
with existing code and will be dropped in the near future.
|
shift |
An integer vector (recycled to the length of x) specifying how
each element in x should be (horizontally) shifted before
the coverage is computed.
|
width |
The length of the returned coverage vector.
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 |
An integer vector specifying how much each element in x counts.
|
... |
Further arguments to be passed to or from other methods. |
An Rle object representing the coverage of x.
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.
The interface of the coverage generic is currently being migrated
from "start/end" to "shift/width".
In the near future, the start and end arguments will be
dropped and the remaining arguments will be:
coverage(x, shift=0L, width=NULL, weight=1L, ...)
The "shift/width" interface is more intuitive, more convenient and
offers slighty more control than the "start/end" interface.
Also it makes sense to add the weight argument to the generic
(vs having it supported only by some methods) since weighting the
elements in x can be considered part of the concept of coverage
in general.
H. Pages and P. Aboyoun
IRanges-class, Views-class, Rle-class, MaskCollection-class
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)