modifyNucleotides {Modstrings} | R Documentation

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

### Description

`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

### Usage

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

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

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

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

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

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

    ## S4 method for signature '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")
    mseq1 <- modifyNucleotides(seq,c(1,2,4),c("1mA","7mG","3mC"))
    # This fails since m7G requires a G at the selected position in the sequence
    ## Not run:
    mseq <- modifyNucleotides(seq,c(3),c("7mG"))

    ## End(Not run)

    # modify nucleotides in a ModRNAString
    seq <- ModRNAString("AGUC")
    mseq1 <- modifyNucleotides(seq,c(1,2,4),c("m1A","m7G","m3C"))
    # This fails since m7G requires a G at the selected position in the sequence
    ## Not run:
    mseq <- modifyNucleotides(seq,c(3),c("m7G"))

    ## End(Not run)

[Package Modstrings version 1.3.12 Index]