| coverage {IRanges} | R Documentation |
Counts the number of times a position is represented in a set of ranges.
coverage(x, start=NA, end=NA, ...) ## S4 method for signature 'IRanges': coverage(x, start=NA, end=NA, weight=1L)
x |
An IRanges or MaskCollection object. |
start |
A single integer specifying the position in x where to start the
extraction of the coverage.
|
end |
A single integer specifying the position in x where to end the
extraction of the coverage.
|
weight |
An integer vector specifying how much each element in x counts.
|
... |
Further arguments to be passed to or from other methods. |
An XRleInteger object representing the coverage of x in the
interval specified by the start and end arguments. An integer
value called the "coverage" can be associated to each position in x,
indicating how many times this position is covered by the ranges stored in
x. Note that the positions in the returned XInteger object are
to be interpreted as relative to the interval specified by the start
and end arguments.
XRleInteger-class, IRanges-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, start=-6, end=20) # 'start' and 'end' must be specified for
# an IRanges object.
coverage(shift(x, 2), start=-6, end=20)
coverage(restrict(x, 1, 10), start=-6, end=20)
coverage(reduce(x), start=-6, end=20)
coverage(gaps(x, start=-6, end=20), start=-6, end=20)
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)