reverseSeq {Biostrings} | R Documentation |
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
reverseSeq(seq) revcompDNA(seq) revcompRNA(seq)
seq |
Character vector. For revcompRNA and
revcompDNA the sequence should consist of appropriate letter
codes: [ACGUN] and ACGTN , respectively. |
The function reverses the order of the constituent character strings of its argument.
A character vector of the same length as seq
.
R. Gentleman, W. Huber, S. Falcon
alphabetFrequency
, reverseComplement
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)) }