Views-class {IRanges} | R Documentation |
The Views virtual class is a general container for storing a set of views on an arbitrary Sequence object, called the "subject".
Its primary purpose is to introduce concepts and provide some facilities that can be shared by the concrete classes that derive from it.
Some direct subclasses of the Views class are: XIntegerViews, RleViews, XStringViews (defined in the Biostrings package), etc...
Views(subject, start=NULL, end=NULL, width=NULL, names=NULL)
:
This constructor is a generic function with dispatch on argument
subject
. Specific methods must be defined for the subclasses
of the Views class. For example a method for
XString subjects is defined
in the Biostrings package that returns an
XStringViews
object. There is no default method.
The treatment of the start
, end
and width
arguments is the same as with the IRanges
constructor,
except that, in addition, Views
allows start
to be a
Ranges object. With this feature,
Views(subject, IRanges(my_starts, my_ends, my_widths, my_names))
and Views(subject, my_starts, my_ends, my_widths, my_names)
are equivalent (except when my_starts
is itself a
Ranges object).
In the code snippets below, from
is a Views object:
as(from, "IRanges")
: Creates an IRanges
object
containing the view locations in from
.
All the accessor-like methods defined for IRanges
objects
work on Views objects. In addition, the following accessors are defined
for Views objects:
subject(x)
:
Return the subject of the views.
"["
, c
and "[["
work on a Views object.
The first two operations are just inherited from the
IRanges
class but now they return a Views object.
However, the "[["
method for Views objects has a
different semantic than the method for IRanges
objects.
x[[i]]
:
Extracts the view selected by i
as an object of the same class
as subject(x)
. Subscript i
can be a single integer
or a character string.
The result is the subsequence of subject(x)
defined by
window(subject(x), start=start(x)[i], end=end(x)[i])
or an error if the view is "out of limits" (i.e. start(x)[i] < 1
or end(x)[i] > length(subject(x))
).
trim(x, use.names=TRUE)
:
Equivalent to
restrict(x, start=1L, end=length(subject(x)), keep.all.ranges=TRUE,
use.names=use.names)
.
subviews(x, start=NA, end=NA, width=NA, use.names=TRUE)
:
start
, end
, and width
arguments must be vectors
of integers, eventually with NAs, that contain coordinates relative
to the current ranges. Equivalent to
trim(narrow(x, start=start, end=end, width=width, use.names=use.names))
.
gaps(x, start=NA, end=NA)
:
start
and end
can be single integers or NAs.
The gap extraction will be restricted to the window specified by
start
and end
. start=NA
and end=NA
are interpreted as start=1
and end=length(subject(x))
,
respectively, so, if start
and end
are not specified,
then gaps are extracted with respect to the entire subject.
successiveViews(subject, width, gapwidth=0, from=1)
:
Equivalent to Views(subject, successiveIRanges(width, gapwidth, from))
.
See ?successiveIRanges
for a description of the width
,
gapwidth
and from
arguments.
H. Pages
IRanges-class, Sequence-class, IRanges-utils, XVector.
Some direct subclasses of the Views class: XIntegerViews-class, RleViews-class, XStringViews-class.
showClass("Views") # shows (some of) the known subclasses ## Create a set of 4 views on an XInteger subject of length 10: subject <- XInteger(10, 3:-6) v1 <- Views(subject, start=4:1, end=4:7) ## Extract the 2nd view: v1[[2]] ## Some views can be "out of limits" v2 <- Views(subject, start=4:-1, end=6) trim(v2) subviews(v2, end=-2) ## gaps() v3 <- Views(subject, start=c(8, 3), end=c(14, 4)) gaps(v3) ## Views on a big XInteger subject: subject <- XInteger(99999, sample(99, 99999, replace=TRUE) - 50) v4 <- Views(subject, start=1:99*1000, end=1:99*1001) v4 v4[-1] v4[[5]] ## 31 adjacent views: successiveViews(subject, 40:10)