XStringViews-class {Biostrings}R Documentation

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).

Usage

  ## Constructors:

  ## S4 method for signature 'character':
  Views(subject, start=NA, end=NA, names=NULL)
  ## S4 method for signature 'XString':
  Views(subject, start=NA, end=NA, names=NULL)

Arguments

subject The subject sequence.
start, end Integer vectors specifying the starting and ending positions of each view.
names If not NULL, the names to assign to each view.

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.

Accesor methods

In the code snippets below, x is an XStringViews object.

subject(x): The subject of x. This is always an XString object.
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, check.limits): Convert x to a character vector of the same length as x. use.names controls whether or not names(x) should be used to set the names of the returned vector (default is TRUE). check.limits controls whether or not an error should be raised if x contains "out of limit" views (default is TRUE). With check.limits=FALSE then "out of limit" views are padded with spaces.
as.matrix(x, mode, use.names, check.limits): Depending on what mode is chosen ("integer" or "character"), return either a 2-column integer matrix containing start(x) and end(x) or a character matrix containing the "exploded" representation of the views. mode="character" can only be used on an XStringViews object with equal-width views. Arguments use.names and check.limits are ignored with mode="integer". With mode="character", use.names controls whether or not names(x) should be used to set the row names of the returned matrix (default is TRUE), and check.limits controls whether or not an error should be raised if x contains "out of limit" views (default is TRUE). With check.limits=FALSE then "out of limit" views are padded with spaces.
toString(x): Equivalent to toString(as.character(x)).

Author(s)

H. Pages

See Also

Views-class, gaps, XStringViews-constructors, 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
  Views("abcdefghij", start=2:1, end=4)
  Views("abcdefghij", start=5:7)
  Views("abcdefghij", end=5:7)

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

[Package Biostrings version 2.10.22 Index]