Replacing letters in a nucleotide sequence (or set of nucleotide sequences) at some specified locations containing nucleotide modifications

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 ModString
replaceLetterAt(x, at, letter, verbose = FALSE)

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

Arguments

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.

Value

the input ModString or ModStringSet

object with the changes applied

Examples

# Replacing the last two letters in a ModDNAString
seq1 <- ModDNAString("AGTC")
seq
#> function (...) 
#> UseMethod("seq")
#> <bytecode: 0x55e2989327a8>
#> <environment: namespace:base>
seq2 <- replaceLetterAt(seq1,c(3,4),"CT")
seq2
#> 4-letter ModDNAString object
#> seq: AGCT

# Now containg and m3C
seq2 <- replaceLetterAt(seq1,c(3,4),ModDNAString("/T"))
seq2
#> 4-letter ModDNAString object
#> seq: AG/T

# Replacing the last two letters in a set of sequences
set1 <- ModDNAStringSet(c("AGTC","AGTC"))
set1
#>   A ModDNAStringSet instance of length 2
#>     width seq
#> [1]     4 AGTC
#> [2]     4 AGTC

set2 <- replaceLetterAt(set1,
                          matrix(rep(c(FALSE,FALSE,TRUE,TRUE),2),
                                 nrow = 2,
                                 byrow = TRUE),
                          c("CT","CT"))
set2
#>   A ModDNAStringSet instance of length 2
#>     width seq
#> [1]     4 AGCT
#> [2]     4 AGCT