R/Modstrings.R
Modstrings.RdRepresenting nucleotide modifications in a nucleotide sequence is usually
done via special characters from a number of sources. This represents a
challenge to work with in R and the Biostrings package. The
Modstrings package implements this functionallity for RNA and DNA
sequences containing modified nucleotides by translating the character
internally in order to work with the infrastructure of the Biostrings
package. For this the ModRNAString and ModDNAString classes and
derivates and functions to construct and modify these objects despite the
encoding issues are implemenented. In addition the conversion from sequences
to list like location information (and the reverse operation) is implemented
as well.
A good place to start would be the vignette and the man page for the
ModStringSet objects.
The alphabets for the modifications used in this package are based on the compilation of RNA modifications by http://modomics.genesilico.pl by the Bujnicki lab and DNA modifications https://dnamod.hoffmanlab.org by the Hoffman lab. Both alphabets were modified to remove some incompatible characters.