XStringViews-constructors {Biostrings}R Documentation

Basic functions for creating or modifying XStringViews objects

Description

A set of basic functions for creating or modifying XStringViews objects.

Usage

  views(subject, start=NA, end=NA)
  adjacentViews(subject, width, gapwidth=0)
  XStringViews(x, subjectClass, collapse="")
  trim(x, use.names=TRUE)
  subviews(x, start=NA, end=NA, width=NA, use.names=TRUE)

Arguments

subject An XString object or a single string.
start An integer vector containing the start positions of the views.
end An integer vector containing the end positions of the views.
width An integer vector containing the widths of the views.
gapwidth An integer vector containing the widths of the gaps between the views.
x An XString object or a character vector for XStringViews. An XStringViews object for trim and subviews.
subjectClass The class to be given to the subject of the XStringViews object created and returned by the function. Must be the name of one of the direct XString subtypes i.e. "BString", "DNAString", "RNAString" or "AAString".
collapse An optional character string to be inserted between the views of the XStringViews object created and returned by the function.
use.names [TODO]

Details

The views function returns an XStringViews object containing views on subject with start and end positions given in the start and end vectors.

The adjacentViews function returns an XStringViews object containing views on subject with widths given in the width vector and separated by gaps of width gapwidth. The first view starts at position 1.

The XStringViews constructor will try to create an XStringViews object from the value passed to its x argument. If x itself is an XStringViews object, the returned object is obtained by coercing its subject to the class specified by subjectClass. If x is an XString object, the returned object is made of a single view that starts at the first letter and ends at the last letter of x (in addition x itself is coerced to the class specified by subjectClass when specified). If x is a character vector, the returned object has one view per character string in x (and its subject is an instance of the class specified by subjectClass).

Value

All these functions return an XStringViews object y with the following number of views (length(y)): max(length(start), length(end) for the views function and length(width) for the adjacentViews function. For the XStringViews constructor, length(y) is 1 when x is an XString object and length(x) otherwise.

See Also

XStringViews-class, XString-class, gaps

Examples

  ## 'start' and 'end' are recycled
  views("abcdefghij", 2:1, 4)
  views("abcdefghij", 5:7, )
  views("abcdefghij", , 5:7)

  ## Views can be "out of limits"
  views("abcdefghij", 2:0, 4)

  ## Views on a DNAString object
  v12 <- views(DNAString("TAATAATG"), -2:9, 0:11)

  ## Creating adjacent views
  v3 <- adjacentViews("abcdefghij", 4:2, gapwidth=1)

  XStringViews(v12, subjectClass="RNAString")
  XStringViews(AAString("MARKSLEMSIR*"))
  XStringViews("abcdefghij", subjectClass="BString")

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

[Package Biostrings version 2.8.18 Index]