Description Usage Arguments Details Value See Also Examples
Use these functions for reversing sequences and/or complementing DNA or RNA sequences.
1 2 | complement(x, ...)
reverseComplement(x, ...)
|
x |
A DNAString, RNAString,
DNAStringSet, RNAStringSet,
XStringViews (with DNAString or RNAString subject),
MaskedDNAString or MaskedRNAString object
for |
... |
Additional arguments to be passed to or from methods. |
See ?reverse
for reversing an XString,
XStringSet or XStringViews object.
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.
reverse,
DNAString-class,
RNAString-class,
DNAStringSet-class,
RNAStringSet-class,
XStringViews-class,
MaskedXString-class,
chartr
,
findPalindromes
,
IUPAC_CODE_MAP
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 | ## ---------------------------------------------------------------------
## A. SOME SIMPLE EXAMPLES
## ---------------------------------------------------------------------
x <- DNAString("ACGT-YN-")
reverseComplement(x)
library(drosophila2probe)
probes <- DNAStringSet(drosophila2probe)
probes
alphabetFrequency(probes, collapse=TRUE)
rcprobes <- reverseComplement(probes)
rcprobes
alphabetFrequency(rcprobes, collapse=TRUE)
## ---------------------------------------------------------------------
## B. OBTAINING THE MISMATCH PROBES OF A CHIP
## ---------------------------------------------------------------------
pm2mm <- function(probes)
{
probes <- DNAStringSet(probes)
subseq(probes, start=13, end=13) <- complement(subseq(probes, start=13, end=13))
probes
}
mmprobes <- pm2mm(probes)
mmprobes
alphabetFrequency(mmprobes, collapse=TRUE)
## ---------------------------------------------------------------------
## C. SEARCHING THE MINUS STRAND OF A CHROMOSOME
## ---------------------------------------------------------------------
## Applying reverseComplement() to the pattern before calling
## matchPattern() is the recommended way of searching hits on the
## minus 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
}
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