XVector: XIntegerViews-class – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

XIntegerViews-class

The XIntegerViews class

Description

The XIntegerViews class is the basic container for storing a set of views (start/end locations) on the same XInteger object.

Details

An XIntegerViews object contains a set of views (start/end locations) on the same XInteger object called "the subject integer vector" or simply "the subject". Each view is defined by its start and end locations: both are integers such that start <= end. An XIntegerViews object is in fact a particular case of a Views object (the XIntegerViews class contains the Views class) so it can be manipulated in a similar manner: see ?Views for more information. Note that two views can overlap and that a view can be "out of limits" i.e. it can start before the first element of the subject or/and end after its last element.

Other methods

In the code snippets below, x, object, e1 and e2 are XIntegerViews objects, and i can be a numeric or logical vector.

: x[[i]]: Extract a view as an XInteger object. i must be a single numeric value (a numeric vector of length 1). Can't be used for extracting a view that is "out of limits" (raise an error). The returned object has the same XInteger subtype as subject(x).
: e1 == e2: A vector of logicals indicating the result of the view by view comparison. The views in the shorter of the two XIntegerViews object being compared are recycled as necessary.
: e1 != e2: Equivalent to !(e1 == e2).

Author(s)

P. Aboyoun

Examples

## One standard way to create an XIntegerViews object is to use
## the Views() constructor:
subject <- as(c(45, 67, 84, 67, 45, 78), "XInteger")
v4 <- Views(subject, start=3:0, end=5:8)
v4
subject(v4)
length(v4)
start(v4)
end(v4)
width(v4)

## Attach a comment to views #3 and #4:
names(v4)[3:4] <- "out of limits"
names(v4)

## A more programatical way to "tag" the "out of limits" views:
idx <- start(v4) < 1 | end(v4) > length(subject(v4)) 
names(v4)[idx] <- "out of limits"

## Extract a view as an XInteger object:
v4[[2]]

## It is an error to try to extract an "out of limits" view:
## Not run: 
v4[[3]] # Error!

## End(Not run)

## Here the first view doesn't even overlap with the subject:
subject <- as(c(97, 97, 97, 45, 45, 98), "XInteger")
Views(subject, start=-3:4, end=-3:4 + c(3:6, 6:3))

## Views on a big XInteger subject:
subject <- XInteger(99999, sample(99, 99999, replace=TRUE) - 50)
v5 <- Views(subject, start=1:99*1000, end=1:99*1001)
v5
v5[-1]
v5[[5]]

## 31 adjacent views:
successiveViews(subject, 40:10)

XVector

Foundation of external vector representation and manipulation in Bioconductor

v0.30.0

Artistic-2.0

Authors

Hervé Pagès and Patrick Aboyoun

Initial release