
"chartr"(old, new, x)
x
is an XString, XStringSet, XStringViews
or MaskedXString object, then the appropriate chartr
method
is called, otherwise the standard chartr
R function
is called.
?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.
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)
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