Views-class: Views objects

In Bioconductor/IRanges: Foundation of integer range manipulation in Bioconductor

Views objects

Description

The Views virtual class is a general container for storing a set of views on an arbitrary Vector 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: RleViews, XIntegerViews (defined in the XVector package), XStringViews (defined in the Biostrings package), etc...

Constructor

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 an IntegerRanges 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 IntegerRanges object).

Coercion

In the code snippets below, from is a Views object:

as(from, "IRanges"):

Creates an IRanges object containing the view locations in from.

Accessor-like methods

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.

Subsetting

x[i]:

Select the views specified by i.

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))).

Concatenation

c(x, ..., ignore.mcols=FALSE):

Concatenate Views objects. They must have the same subject.

Other methods

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)).

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.

Author(s)

Hervé Pagès

See Also

IRanges-class, Vector-class, IRanges-utils, XVector.

Some direct subclasses of the Views class: RleViews-class, XIntegerViews-class, XDoubleViews-class, XStringViews-class.

findOverlaps.

Examples

showClass("Views")  # shows (some of) the known subclasses

## Create a set of 4 views on an XInteger subject of length 10:
subject <- Rle(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)

## See ?`XIntegerViews-class` in the XVector package for more examples.

Bioconductor/IRanges documentation built on Dec. 7, 2024, 1:19 p.m.