Modifying nucleotides in a nucleotide sequence (or set of sequences) at specified locations

modifyNucleotides modifies a nucleotide in a sequence (or set of sequences) based on the type of modification provided. It checks for the identity of the base nucleotide to be

modifyNucleotides(
  x,
  at,
  mod,
  nc.type = "short",
  stop.on.error = TRUE,
  verbose = FALSE
)

# S4 method for ModString
modifyNucleotides(
  x,
  at,
  mod,
  nc.type = c("short", "nc"),
  stop.on.error = TRUE,
  verbose = FALSE
)

# S4 method for ModStringSet
modifyNucleotides(
  x,
  at,
  mod,
  nc.type = c("short", "nc"),
  stop.on.error = TRUE,
  verbose = FALSE
)

# S4 method for DNAString
modifyNucleotides(
  x,
  at,
  mod,
  nc.type = c("short", "nc"),
  stop.on.error = TRUE,
  verbose = FALSE
)

# S4 method for RNAString
modifyNucleotides(
  x,
  at,
  mod,
  nc.type = c("short", "nc"),
  stop.on.error = TRUE,
  verbose = FALSE
)

# S4 method for DNAStringSet
modifyNucleotides(
  x,
  at,
  mod,
  nc.type = c("short", "nc"),
  stop.on.error = TRUE,
  verbose = FALSE
)

# S4 method for RNAStringSet
modifyNucleotides(
  x,
  at,
  mod,
  nc.type = c("short", "nc"),
  stop.on.error = TRUE,
  verbose = FALSE
)

Arguments

x

a ModString or ModStringSet object

at

the location where the modification should be made.

The same input as in the original 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.

mod

The modification short name or nomenclature

If x is a ModString object, then letter must be a ModString object or a character vector (with no NA) 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, a list of character vectors or a CharacterList 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))).

nc.type

the type of nomenclature to be used. Either "short" or "nc". "Short" for m3C would be "m3C", "nc" for m3C would be "3C". ( default = "short")

stop.on.error

For combineIntoModstrings: TRUE(default) or FALSE: Should an error be raised upon encounter of incompatible positions?

verbose

See replaceLetterAt.

Value

the input ModString or ModStringSet

object with the changes applied

Examples

# modify nucleotides in a ModDNAString 
seq <- ModDNAString("AGTC")
seq
#> 4-letter ModDNAString object
#> seq: AGTC

mseq1 <- modifyNucleotides(seq,c(1,2,4),c("1mA","7mG","3mC"))
mseq1
#> 4-letter ModDNAString object
#> seq: "7T'

# This fails since m7G requires a G at the selected position in the sequence
if (FALSE) {
mseq <- modifyNucleotides(seq,c(3),c("7mG"))
}

# modify nucleotides in a ModRNAString 
seq <- ModRNAString("AGUC")
seq
#> 4-letter ModRNAString object
#> seq: AGUC

mseq1 <- modifyNucleotides(seq,c(1,2,4),c("m1A","m7G","m3C"))
mseq1
#> 4-letter ModRNAString object
#> seq: "7U'

# This fails since m7G requires a G at the selected position in the sequence
if (FALSE) {
mseq <- modifyNucleotides(seq,c(3),c("m7G"))
}