modifyNucleotides {Modstrings} | R Documentation |
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 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 )
x |
a |
at |
the location where the modification should be made. The same input as in the original If x is a If x is a rectangular |
mod |
The modification short name or nomenclature If If |
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". (
|
stop.on.error |
For |
verbose |
See |
the input ModString
or ModStringSet
object with the changes applied
# 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)