replaceLetterAt: Replacing letters in a nucleotide sequence (or set of...

In FelixErnst/Modstrings: Working with modified nucleotide sequences

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

Description

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

Usage

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

## S4 method for signature '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
seq2 <- replaceLetterAt(seq1,c(3,4),"CT")
seq2

# Now containg and m3C
seq2 <- replaceLetterAt(seq1,c(3,4),ModDNAString("/T"))
seq2

# Replacing the last two letters in a set of sequences
set1 <- ModDNAStringSet(c("AGTC","AGTC"))
set1

set2 <- replaceLetterAt(set1,
                          matrix(rep(c(FALSE,FALSE,TRUE,TRUE),2),
                                 nrow = 2,
                                 byrow = TRUE),
                          c("CT","CT"))
set2

FelixErnst/Modstrings documentation built on April 1, 2024, 2:21 p.m.