modifyNucleotides | 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")
seq
mseq1 <- modifyNucleotides(seq,c(1,2,4),c("1mA","7mG","3mC"))
mseq1
# 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")
seq
mseq1 <- modifyNucleotides(seq,c(1,2,4),c("m1A","m7G","m3C"))
mseq1
# 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)
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