subXString {Biostrings}R Documentation

Fast substring extraction

Description

Functions for fast substring extraction.

Usage

  subXString(x, start=NA, end=NA, length=NA)
  substr(x, start=NA, stop=NA)
  substring(text, first=NA, last=NA)

Arguments

x An XString object for subXString. A character vector, an XStringViews or an XString object for substr or substring.
start A numeric vector.
end A numeric vector.
length A numeric vector.
stop A numeric vector.
text A character vector, an XStringViews or an XString object.
first A numeric vector.
last A numeric vector.

Details

subXString provides a very efficient way to extract a substring from an XString object. For example, extracting a 100Mb substring from Human chromosome 1 (250Mb) with subXString is almost instantaneous and has almost no memory footprint. In fact, the cost in time and memory of a call to subXString doesn't depend on the length of the original object or on the length of the extracted object. The "trick" behind this "feature" is very simple: subXString does NOT copy the sequence data.

Value

[TODO]

Author(s)

H. Pages

See Also

letter, views, XString-class, XStringViews-class

Examples

  subXString("AxyxyxBC", 7)
  s <- BString("AxyxyxBC")
  subXString(s, 7)  # same as subXString("AxyxyxBC", 7)
  subXString(s, , 7)
  subXString(s, , 7, 3)
  identical(subXString(s), s) # TRUE

  v <- views(s, c(6, 4,-1, NA), c(7, 6, 1, 1))
  ## 2 equivalent ways of keeping the last letter of each view
  views(subject(v), end(v), end(v))

  ## 2 equivalent ways of making the views wider
  views(subject(v), start(v)-3, end(v)+3)

[Package Biostrings version 2.8.18 Index]