reverseSeq {Biostrings}R Documentation

Reverse Sequence

Description

WARNING: The functions described in this man page have been deprecated in favor of reverse,XString-method and reverseComplement.

Functions to obtain the reverse and reverse complement of a sequence

Usage

reverseSeq(seq)
revcompDNA(seq)
revcompRNA(seq)

Arguments

seq Character vector. For revcompRNA and revcompDNA the sequence should consist of appropriate letter codes: [ACGUN] and ACGTN, respectively.

Details

The function reverses the order of the constituent character strings of its argument.

Value

A character vector of the same length as seq.

Author(s)

R. Gentleman, W. Huber, S. Falcon

See Also

alphabetFrequency, reverseComplement

Examples

 w <-  c("hey there", "you silly fool")
 if (interactive()) {
   reverseSeq(w)  # deprecated (inefficient on large vectors)
 }
 reverse(BStringSet(w))  # more efficient

 w <- "able was I ere I saw Elba"
 if (interactive()) {
   reverseSeq(w)  # deprecated (inefficient on large vectors)
 }
 reverse(BStringSet(w))  # more efficient

 rna1 <- "UGCA"
 if (interactive()) {
   revcompRNA(rna1)  # deprecated (inefficient on large vectors)
 }
 reverseComplement(RNAString(rna1))  # more efficient

 dna1 <- "TGCA"
 if (interactive()) {
   revcompDNA(dna1)  # deprecated (inefficient on large vectors)
 }
 reverseComplement(DNAString(dna1))  # more efficient

 ## Comparing efficiencies:
 if (interactive()) {
   library(hgu95av2probe)
   system.time(y1 <- reverseSeq(hgu95av2probe$sequence))
   x <- DNAStringSet(hgu95av2probe)
   system.time(y2 <- reverse(x))

   system.time(y3 <- revcompDNA(hgu95av2probe$sequence))
   system.time(y4 <- reverseComplement(x))
 }

[Package Biostrings version 2.14.12 Index]