| chartr {Biostrings} | R Documentation |
Translate letters of a sequence.
## S4 method for signature 'ANY,ANY,XString' chartr(old, new, x)
old |
A character string specifying the characters to be translated. |
new |
A character string specifying the translations. |
x |
The sequence or set of sequences to translate.
If |
See ?chartr for the details.
Note that, unlike the standard chartr R function,
the methods for XString, XStringSet, XStringViews
and MaskedXString objects do NOT support character ranges in the
specifications.
An object of the same class and length as the original object.
chartr,
replaceLetterAt,
XString-class,
XStringSet-class,
XStringViews-class,
MaskedXString-class,
alphabetFrequency,
matchPattern,
reverseComplement
x <- BString("MiXeD cAsE 123")
chartr("iXs", "why", x)
## ---------------------------------------------------------------------
## TRANSFORMING DNA WITH BISULFITE (AND SEARCHING IT...)
## ---------------------------------------------------------------------
library(BSgenome.Celegans.UCSC.ce2)
chrII <- Celegans[["chrII"]]
alphabetFrequency(chrII)
pattern <- DNAString("TGGGTGTATTTA")
## Transforming and searching the + strand
plus_strand <- chartr("C", "T", chrII)
alphabetFrequency(plus_strand)
matchPattern(pattern, plus_strand)
matchPattern(pattern, chrII)
## Transforming and searching the - strand
minus_strand <- chartr("G", "A", chrII)
alphabetFrequency(minus_strand)
matchPattern(reverseComplement(pattern), minus_strand)
matchPattern(reverseComplement(pattern), chrII)