ModRNAString: ModDNAString class
In Modstrings: Working with modified nucleotide sequences

Description Usage Arguments Details Value Examples

A ModRNAString object allows RNA sequences with modified nucleotides to be stored and manipulated.

1	ModRNAString(x = "", start = 1, nchar = NA)

`x`	the input as a `character`.
`start`	the postion in the character vector to use as start position in the `ModRNAString` object (default `start = 1`).
`nchar`	the width of the character vector to use in the `ModRNAString` object (default `nchar = NA`). The end position is calculated as `start + nchar - 1`.

The ModRNAString class contains the virtual ModString class, which is itself based on the XString class. Therefore, functions for working with XString classes are inherited.

The alphabet of the ModRNAString class consist of the non-extended IUPAC codes "A,G,C,U", the gap letter "-", the hard masking letter "+", the not available letter "." and letters for individual modifications: alphabet(ModRNAString()).

Since the special characters are encoded differently depending on the OS and encoding settings of the R session, it is not always possible to enter a RNA sequence containing modified nucleotides via the R console. The most convinient solution for this problem is to use the function modifyNucleotides and modify and existing RNAString or ModRNAString object.

A ModRNAString object can be converted into a RNAString object using the RNAstring() constructor. Modified nucleotides are automaitcally converted intro their base nucleotides.

If a modified RNA nucleotide you want to work with is not part of the alphabet, please let us know.

a ModRNAString object

# Constructing ModDNAString containing an m6A and a dihydrouridine
mr1 <- ModRNAString("AGCU`D")

# the alphabet of the ModRNAString class
alphabet(mr1)
# due to encoding issues the shortNames can also be used
shortName(mr1)
# due to encoding issues the nomenclature can also be used
nomenclature(mr1)

# convert to RNAString
r1 <- RNAString(mr1)