Description Usage Arguments Value Examples
The ModStringSet
class is a container for storing a set of
ModString
objects. It follows the same principles as the
other XStringSet
objects.
As usual the ModStringSet
containers derive directly from the
XStringSet
virtual class.
The ModStringSet
class is in itself a virtual class with two types of
derivates:
ModDNAStringSet
ModRNAStringSet
Each class can only be converted to its parent DNAStringSet
or
RNAStringSet
. The modified nucleotides will be converted to their
original nucleotides.
Please note, that due to encoding issues not all modifications can be instanciated directly from the console. The vignette contains a comphrensive explanation and examples for working around the problem.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 |
x |
Either a character vector (with no NAs), or an ModString, ModStringSet or ModStringViews object. |
start, end, width |
Either NA, a single integer, or an integer vector of the same length as x specifying how x should be "narrowed" (see ?narrow for the details). |
use.names |
TRUE or FALSE. Should names be preserved? |
a ModStringSet
object.
1 2 3 4 5 6 7 8 9 | # Constructing ModDNAStringSet containing an m6A
m1 <- ModDNAStringSet(c("AGCT`","AGCT`"))
m1
# converting to DNAStringSet
# Constructing ModRNAStringSet containing an m6A
m2 <- ModRNAStringSet(c("AGCU`","AGCU`"))
m2
|
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