coverage {IRanges} | R Documentation |
Counts the number of times a position is represented in a set of ranges.
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)))
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
For example, when
When
When |
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 .
|
... |
Further arguments to be passed to or from other methods. |
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.
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)