replaceLetterAt: Replacing letters in a nucleotide sequence (or set of...
In Modstrings: Working with modified nucleotide sequences

Description Usage Arguments Value Examples

replaceLetterAt replaces a letter in a ModString objects with a new letter. In contrast to modifyNucleotides it does not check the letter to be replaced for its identity, it just replaces it and behaves exactly like the

## S4 method for signature 'ModString'
replaceLetterAt(x, at, letter, verbose = FALSE)

## S4 method for signature 'ModStringSet'
replaceLetterAt(x, at, letter, verbose = FALSE)

`x`	a `ModString` or `ModStringSet` object
`at`	the location where the replacement should be made. The same input as in `replaceLetterAt` are expected: If x is a `ModString` object, then at is typically an integer vector with no NAs but a logical vector or Rle object is valid too. Locations can be repeated and in this case the last replacement to occur at a given location prevails. If x is a rectangular `ModStringSet` object, then `at` must be a matrix of logicals with the same dimensions as x. If the `ModStringSet` is not rectangular, `at` must be a list of logical vectors.
`letter`	The new letters. The same input as in `replaceLetterAt` are expected: If x is a `ModString` object, then letter must be a `ModString` object or a character vector (with no NAs) with a total number of letters (sum(nchar(letter))) equal to the number of locations specified in at. If x is a rectangular `ModStringSet` object, then letter must be a `ModStringSet` object or a character vector of the same length as x. In addition, the number of letters in each element of letter must match the number of locations specified in the corresponding row of at (all(width(letter) == rowSums(at))).
`verbose`	See `replaceLetterAt`.

the input ModString or ModStringSet object with the changes applied

# Replacing the last two letters in a ModDNAString
seq1 <- ModDNAString("AGTC")
seq2 <- replaceLetterAt(seq1,c(3,4),"CT")
# Now containg and m3C
seq2 <- replaceLetterAt(seq1,c(3,4),ModDNAString("/T"))
# Replacing the last two letters in a set of sequences
set1 <- ModDNAStringSet(c("AGTC","AGTC"))
set2 <- replaceLetterAt(set1,
                          matrix(rep(c(FALSE,FALSE,TRUE,TRUE),2),
                                 nrow = 2,
                                 byrow = TRUE),
                          c("CT","CT"))