findPalindromes {Biostrings} | R Documentation |
The findPalindromes
and findComplementedPalindromes
functions can be used to find palindromic or complemented palindromic
regions in a sequence.
palindromeArmLength
, palindromeLeftArm
,
palindromeRightArm
,
complementedPalindromeArmLength
, complementedPalindromeLeftArm
and complementedPalindromeRightArm
are utility functions for
operating on palindromic or complemented palindromic sequences.
findPalindromes(subject, min.armlength=4, max.looplength=1, min.looplength=0, max.mismatch=0) palindromeArmLength(x, max.mismatch=0, ...) palindromeLeftArm(x, max.mismatch=0, ...) palindromeRightArm(x, max.mismatch=0, ...) findComplementedPalindromes(subject, min.armlength=4, max.looplength=1, min.looplength=0, max.mismatch=0) complementedPalindromeArmLength(x, max.mismatch=0, ...) complementedPalindromeLeftArm(x, max.mismatch=0, ...) complementedPalindromeRightArm(x, max.mismatch=0, ...)
subject |
An XString object containing the subject string, or an XStringViews object. |
min.armlength |
An integer giving the minimum length of the arms of the palindromes (or complemented palindromes) to search for. |
max.looplength |
An integer giving the maximum length of "the loop" (i.e the sequence
separating the 2 arms) of the palindromes (or complemented palindromes)
to search for.
Note that by default (max.looplength=1 ), findPalindromes
will search for strict palindromes (or complemented palindromes) only.
|
min.looplength |
An integer giving the minimum length of "the loop" of the palindromes (or complemented palindromes) to search for. |
max.mismatch |
The maximum number of mismatching letters allowed between the 2 arms of the palindromes (or complemented palindromes) to search for. |
x |
An XString object containing a 2-arm palindrome or complemented palindrome, or an XStringViews object containing a set of 2-arm palindromes or complemented palindromes. |
... |
Additional arguments to be passed to or from methods. |
The findPalindromes
function finds palindromic substrings in a subject
string. The palindromes that can be searched for are either strict palindromes
or 2-arm palindromes (the former being a particular case of the latter) i.e.
palindromes where the 2 arms are separated by an arbitrary sequence called
"the loop".
Use the findComplementedPalindromes
function to find complemented
palindromic substrings in a DNAString subject (in a complemented
palindrome the 2 arms are reverse-complementary sequences).
findPalindromes
and findComplementedPalindromes
return an
XStringViews object containing all palindromes (or complemented
palindromes) found in subject
(one view per palindromic substring
found).
palindromeArmLength
and complementedPalindromeArmLength
return
the arm length (integer) of the 2-arm palindrome (or complemented palindrome)
x
.
It will raise an error if x
has no arms. Note that any sequence could
be considered a 2-arm palindrome if we were OK with arms of length 0 but we
are not: x
must have arms of length greater or equal to 1 in order to
be considered a 2-arm palindrome. The same apply to 2-arm complemented
palindromes.
When applied to an XStringViews object x
,
palindromeArmLength
and complementedPalindromeArmLength
behave
in a vectorized fashion by returning an integer vector of the same length
as x
.
palindromeLeftArm
and complementedPalindromeLeftArm
return an
object of the same class as the original object x
and containing the
left arm of x
.
palindromeRightArm
does the same as palindromeLeftArm
but on
the right arm of x
.
Like palindromeArmLength
, both palindromeLeftArm
and
palindromeRightArm
will raise an error if x
has no arms.
Also, when applied to an XStringViews object x
, both behave
in a vectorized fashion by returning an XStringViews object of the
same length as x
.
H. Pages
maskMotif
,
matchPattern
,
matchLRPatterns
,
matchProbePair
,
XStringViews-class,
DNAString-class
## Note that complemented palindromes (like palindromes) can be nested findComplementedPalindromes(DNAString("ACGTTNAACGT-ACGTTNAACGT")) ## A real use case library(BSgenome.Dmelanogaster.UCSC.dm3) chrX <- Dmelanogaster$chrX chrX_pals <- findComplementedPalindromes(chrX, min.armlength=50, max.looplength=20) complementedPalindromeArmLength(chrX_pals) # 251 ## Of course, whitespaces matter palindromeArmLength(BString("was it a car or a cat I saw")) ## Note that the 2 arms of a strict palindrome (or strict complemented ## palindrome) are equal to the full sequence. palindromeLeftArm(BString("Delia saw I was aileD")) complementedPalindromeLeftArm(DNAString("N-ACGTT-AACGT-N")) palindromeLeftArm(DNAString("N-AAA-N-N-TTT-N"))