chartr {Biostrings} | R Documentation |
Replace letters in a sequence or set of sequences
Description
Replace letters in a sequence or set of sequences.
Usage
## S4 method for signature 'ANY,ANY,XString'
chartr(old, new, x)
replaceAmbiguities(x, new="N")
Arguments
old |
A character string specifying the characters to be replaced. |
new |
A character string specifying the replacements. It must be a single
letter for |
x |
The sequence or set of sequences to translate.
If |
Details
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.
replaceAmbiguities()
is a simple wrapper around chartr()
that replaces all IUPAC ambiguities with N.
Value
An object of the same class and length as the original object.
See Also
-
chartr
in the base package. The
replaceAt
function for extracting or replacing arbitrary subsequences from/in a sequence or set of sequences.The
replaceLetterAt
function for a DNA-specific single-letter replacement functions useful for SNP injections.-
IUPAC_CODE_MAP
for the mapping between IUPAC nucleotide ambiguity codes and their meaning. -
alphabetFrequency
(anduniqueLetters
) for tabulating letters in (and extracting the unique letters from) a sequence or set of sequences. The XString, XStringSet, XStringViews, and MaskedXString classes.
Examples
## ---------------------------------------------------------------------
## A BASIC chartr() EXAMPLE
## ---------------------------------------------------------------------
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)
## ---------------------------------------------------------------------
## replaceAmbiguities()
## ---------------------------------------------------------------------
dna <- DNAStringSet(c("TTTKYTT-GR", "", "NAASACVT"))
dna
replaceAmbiguities(dna)