XStringViews-class: The XStringViews class

In Bioconductor/Biostrings: Efficient manipulation of biological strings

The XStringViews class

Description

The XStringViews class is the basic container for storing a set of views (start/end locations) on the same sequence (an XString object).

Details

An XStringViews object contains a set of views (start/end locations) on the same XString object called "the subject string" or "the subject sequence" or simply "the subject". Each view is defined by its start and end locations: both are integers such that start <= end. An XStringViews object is in fact a particular case of an Views object (the XStringViews 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 letter of the subject or/and end after its last letter.

Constructor

Views(subject, start=NULL, end=NULL, width=NULL, names=NULL):

See ?Views in the IRanges package for the details.

Accessor-like methods

All the accessor-like methods defined for Views objects work on XStringViews objects. In addition, the following accessors are defined for XStringViews objects:

nchar(x):

A vector of non-negative integers containing the number of letters in each view. Values in nchar(x) coincide with values in width(x) except for "out of limits" views where they are lower.

Other methods

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

e1 == e2:

A vector of logicals indicating the result of the view by view comparison. The views in the shorter of the two XStringViews object being compared are recycled as necessary.

Like for comparison between XString objects, comparison between two XStringViews objects with subjects of different classes is not supported with one exception: when the subjects are DNAString and RNAString instances.

Also, like with XString objects, comparison between an XStringViews object with a BString subject and a character vector is supported (see examples below).

e1 != e2:

Equivalent to !(e1 == e2).

as.character(x, use.names=TRUE, check.limits=TRUE):

Converts x to a character vector of the same length as x. The use.names argument controls whether or not names(x) should be propagated to the names of the returned vector. The check.limits argument controls whether or not an error should be raised if x has "out of limit" views. If check.limits is FALSE then "out of limit" views are trimmed with a warning.

as.data.frame(x, row.names = NULL, optional = FALSE, ...)

Equivalent of as.data.frame(as.character(x)).

as.matrix(x, use.names=TRUE):

Returns a character matrix containing the "exploded" representation of the views. Can only be used on an XStringViews object with equal-width views. The use.names argument controls whether or not names(x) should be propagated to the row names of the returned matrix.

toString(x):

Equivalent to toString(as.character(x)).

Author(s)

H. Pagès

See Also

Views-class, gaps, XString-class, XStringSet-class, letter, MIndex-class

Examples

## One standard way to create an XStringViews object is to use
## the Views() constructor.

## Views on a DNAString object:
s <- DNAString("-CTC-N")
v4 <- Views(s, 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:
names(v4)[start(v4) < 1 | nchar(subject(v4)) < end(v4)] <- "out of limits"
## or just:
names(v4)[nchar(v4) < width(v4)] <- "out of limits"

## Two equivalent ways to extract a view as an XString object:
s2a <- v4[[2]]
s2b <- subseq(subject(v4), start=start(v4)[2], end=end(v4)[2])
identical(s2a, s2b) # TRUE

## It is an error to try to extract an "out of limits" view:
#v4[[3]] # Error!

v12 <- Views(DNAString("TAATAATG"), start=-2:9, end=0:11)
v12 == DNAString("TAA")
v12[v12 == v12[4]]
v12[v12 == v12[1]]
v12[3] == Views(RNAString("AU"), start=0, end=2)

## Here the first view doesn't even overlap with the subject:
Views(BString("aaa--b"), start=-3:4, end=-3:4 + c(3:6, 6:3))

## 'start' and 'end' are recycled:
subject <- "abcdefghij"
Views(subject, start=2:1, end=4)
Views(subject, start=5:7, end=nchar(subject))
Views(subject, start=1, end=5:7)

## Applying gaps() to an XStringViews object:
v2 <- Views("abCDefgHIJK", start=c(8, 3), end=c(14, 4))
gaps(v2)

## Coercion:
as(v12, "XStringSet")  # same as 'as(v12, "DNAStringSet")'
rna <- as(v12, "RNAStringSet")
as(rna, "Views")

Bioconductor/Biostrings documentation built on Dec. 16, 2024, 8:46 a.m.