Ranges-utils {IRanges} | R Documentation |
Utility functions for modifying Ranges objects.
flank(x, width, start=TRUE, both=FALSE, use.names=TRUE) narrow(x, start=NA, end=NA, width=NA, use.names=TRUE) reflect(x, bounds, use.names=TRUE) resize(x, width, fix="start", use.names=TRUE, ...) restrict(x, start=NA, end=NA, keep.all.ranges=FALSE, use.names=TRUE) shift(x, shift, use.names=TRUE) ## S4 method for signature 'Ranges': range(x, ..., na.rm = FALSE) ## S4 method for signature 'Ranges': reduce(x, drop.empty.ranges=FALSE, min.gapwidth=1L, with.inframe.attrib=FALSE) threebands(x, start=NA, end=NA, width=NA)
x |
An Ranges object. |
width |
For narrow and threebands , a vector of integers, eventually
with NAs. See the SEW (Start/End/Width) interface for the details
(?solveUserSEW ).
For |
start, end |
A single integer or NA for all functions except narrow ,
threebands , and flank .
For
For |
both |
If TRUE , extends the flanking region width positions
into the range. The resulting range thus straddles the end
point, with width positions on either side.
|
use.names |
TRUE or FALSE . Should names be preserved?
|
bounds |
An IRanges object to serve as the reference bounds for the reflection, see below. |
fix |
For resize , a character vector or character Rle of length 1 or
length(x) containing the values "start" , "end" ,
and "center" denoting what to use as an anchor for each element
in x .
|
keep.all.ranges |
TRUE or FALSE . Should ranges that don't overlap with
the interval specified by start and end be kept?
Note that "don't overlap" means that they end strictly before
start - 1 or start strictly after end + 1 .
Ranges that end at start - 1 or start at end + 1
are always kept and their width is set to zero in the returned
IRanges object.
|
shift |
A single integer. |
drop.empty.ranges |
TRUE or FALSE . Should empty ranges be dropped?
|
min.gapwidth |
Ranges separated by a gap of at least min.gapwidth positions
won't be merged in the Ranges object returned by reduce .
Otherwise, they will.
|
with.inframe.attrib |
TRUE or FALSE . For internal use.
|
... |
For range , additional Ranges to consider.
|
na.rm |
Ignored |
flank
generates flanking ranges for each range in x
. If
start
is TRUE
for a given range, the flanking occurs at
the start, otherwise the end. The widths of the flanks are given by
the width
parameter. The widths can be negative, in which case
the flanking region is reversed so that it represents a prefix or
suffix of the range in x
. The flank
operation is
illustrated below for a call of the form flank(x, 3, TRUE)
,
where x
indicates a range in x
and -
indicates
the resulting flanking region:
---xxxxxxxIf
start
were FALSE
:
xxxxxxx---For negative width, i.e.
flank(x, -3, FALSE)
, where *
indicates the overlap between x
and the result:
xxxx***If
both
is TRUE
, then, for
all ranges in x
, the flanking regions are extended into
(or out of, if width is negative)
the range, so that the result straddles the given endpoint and has
twice the width given by width
. This is illustrated below for
flank(x, 3, both=TRUE)
:
---***xxxx
narrow
narrows the ranges in x
i.e. each range in the
returned Ranges object is a subrange of the corresponding
range in x
.
The supplied start/end/width values are solved by a call to
solveUserSEW(width(x), start=start, end=end, width=width)
and therefore must be compliant with the rules of the SEW
(Start/End/Width) interface (see ?solveUserSEW
for the details).
Then each subrange is derived from the original range according
to the solved start/end/width values for this range. Note that those
solved values are interpreted relatively to the original range.
reflect
"reflects" or reverses each range in x
relative to
the corresponding range in bounds
, which is recycled as
necessary. Reflection preserves the width of a range, but shifts it
such the distance from the left bound to the start of the range
becomes the distance from the end of the range to the right
bound. This is illustrated below, where x
represents
a range in x
and [
and ]
indicate the bounds:
[..xxx.....] becomes [.....xxx..]
resize
resizes the ranges to the specified width where either the
start, end, or center is used as an anchor.
restrict
restricts the ranges in x
to the interval
specified by the start
and end
arguments.
shift
shifts all the ranges in x
.
range
returns an IRanges
instance with a single range,
from the minimum start to the maximum end in the combined ranges of
x
and the arguments in ...
.
reduce
first orders the ranges in x
from left to right,
then merges the overlapping or adjacent ones.
threebands
extends the capability of narrow
by returning
the 3 ranges objects associated to the narrowing operation.
The returned value y
is a list of 3 ranges objects named
"left"
, "middle"
and "right"
.
The middle component is obtained by calling narrow
with the
same arguments (except that names are dropped). The left and right
components are also instances of the same class as x
and they
contain what has been removed on the left and right sides (respectively)
of the original ranges during the narrowing.
Note that original object x
can be reconstructed from the
left and right bands with punion(y$left, y$right, fill.gap=TRUE)
.
H. Pages, M. Lawrence, P. Aboyoun
threebands
could be described as a parallel variant
of disjoin
.
Ranges-class,
IRanges-setops,
solveUserSEW
vec <- as.integer(c(19, 5, 0, 8, 5)) x <- successiveIRanges(vec) x shift(x, -3) restrict(x, start=12, end=34) restrict(x, start=20) restrict(x, start=21) restrict(x, start=21, keep.all.ranges=TRUE) y <- x[width(x) != 0] narrow(y, start=4, end=-2) narrow(y, start=-4, end=-2) narrow(y, end=5, width=3) narrow(y, start = c(3, 4, 2, 3), end = c(12, 5, 7, 4)) resize(y, width = 200) resize(y, width = 2, fix = "end") z <- threebands(y, start=4, end=-2) y0 <- punion(z$left, z$right, fill.gap=TRUE) identical(y, y0) # TRUE threebands(y, start=-5) x <- IRanges(start=c(-2, 6, 9, -4, 1, 0, -6, 3, 10), width=c( 5, 0, 6, 1, 4, 3, 2, 0, 3)) reduce(x) reduce(x, drop.empty.ranges=TRUE) ir1 <- IRanges(c(2,5,1), c(3,7,3)) bounds <- IRanges(c(0, 5, 3), c(10, 6, 9)) reflect(ir1, bounds) flank(ir1, 2) flank(ir1, 2, FALSE) flank(ir1, 2, c(FALSE, TRUE, FALSE)) flank(ir1, c(2, -2, 2)) flank(ir1, 2, both = TRUE) flank(ir1, 2, FALSE, TRUE) flank(ir1, -2, FALSE, TRUE)