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)