reverseComplement {Biostrings} | R Documentation |
Use these functions for reversing a sequence and/or complementing a DNA sequence.
## S4 method for signature 'XString': reverse(x, ...) complement(x, ...) reverseComplement(x, ...)
x |
An IRanges, NormalIRanges, MaskCollection,
XString, XStringSet, XStringViews
or MaskedXString object for reverse .
A DNAString, RNAString, DNAStringSet, RNAStringSet, XStringViews (with DNAString or RNAString subject), MaskedDNAString or MaskedRNAString object for complement and reverseComplement .
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... |
Additional arguments to be passed to or from methods. |
Given an XString object x
, reverse(x)
returns
an object of the same XString subtype as x
where letters
in x
have been reordered in the reverse order.
If x
is a DNAString or RNAString object,
complement(x)
returns an object where each base in x
is "complemented" i.e. A, C, G, T in a DNAString object are replaced
by T, G, C, A respectively and A, C, G, U in a RNAString object
are replaced by U, G, C, A respectively.
Letters belonging to the "IUPAC extended genetic alphabet"
are also replaced by their complement (M <-> K, R <-> Y, S <-> S, V <-> B,
W <-> W, H <-> D, N <-> N) and the gap ("-"
) and hard masking
("+"
) letters are unchanged.
reverseComplement(x)
is equivalent to reverse(complement(x))
but is faster and more memory efficient.
An object of the same class and length as the original object.
IRanges-class,
NormalIRanges-class,
MaskCollection-class,
DNAString-class,
RNAString-class,
DNAStringSet-class,
RNAStringSet-class,
XStringViews-class,
MaskedXString-class,
strrev
,
chartr
,
findPalindromes
## --------------------------------------------------------------------- ## A. SIMPLE EXAMPLES ## --------------------------------------------------------------------- x <- DNAString("ACGT-YN-") reverseComplement(x) library(drosophila2probe) x <- DNAStringSet(drosophila2probe$sequence) x alphabetFrequency(x, collapse=TRUE) rcx <- reverseComplement(x) rcx alphabetFrequency(rcx, collapse=TRUE) ## --------------------------------------------------------------------- ## B. SEARCHING THE REVERSE STRAND OF A CHROMOSOME ## --------------------------------------------------------------------- ## Applying reverseComplement() to the pattern before calling ## matchPattern() is the recommended way to search hits on the reverse ## strand of a chromosome. library(BSgenome.Dmelanogaster.UCSC.dm3) chrX <- Dmelanogaster$chrX pattern <- DNAString("ACCAACNNGGTTG") matchPattern(pattern, chrX, fixed=FALSE) # 3 hits on strand + rcpattern <- reverseComplement(pattern) rcpattern m0 <- matchPattern(rcpattern, chrX, fixed=FALSE) m0 # 5 hits on strand - ## Applying reverseComplement() to the subject instead of the pattern is not ## a good idea for 2 reasons: ## (1) Chromosome sequences are generally big and sometimes very big ## so computing the reverse complement of the positive strand will ## take time and memory proportional to its length. chrXminus <- reverseComplement(chrX) # needs to allocate 22M of memory! chrXminus ## (2) Chromosome locations are generally given relatively to the positive ## strand, even for features located in the negative strand, so after ## doing this: m1 <- matchPattern(pattern, chrXminus, fixed=FALSE) ## the start/end of the matches are now relative to the negative strand. ## You need to apply reverseComplement() again on the result if you want ## them to be relative to the positive strand: m2 <- reverseComplement(m1) # allocates 22M of memory, again! ## and finally to apply rev() to sort the matches from left to right ## (5'3' direction) like in m0: m3 <- rev(m2) # same as m0, finally! ## WARNING: Before you try the example below on human chromosome 1, be aware ## that it will require the allocation of about 500Mb of memory! if (interactive()) { library(BSgenome.Hsapiens.UCSC.hg18) chr1 <- Hsapiens$chr1 matchPattern(pattern, reverseComplement(chr1)) # DON'T DO THIS! matchPattern(reverseComplement(pattern), chr1) # DO THIS INSTEAD }