RNAEdit — RNA editting model

Usage

RNAEdit(submodel: CTMC<b>, edits: Map<String,String>, rnaRate: Double, a: RNAEdits<a>) → CTMC<RNAEdits<a>>

Type constraints: Nucleotides<a>

Arguments

submodel:

Nucleotide rates

edits:

Map from source nucleotide to edited nucleotide

rnaRate:

scaling factor for rates that change the RNA

Default: 1

a:

The RNAEdits alphabet

Default: The alphabet in the current context

Original default expressions
a 
get_state(alphabet)

Description

Rate matrix on a doublets, constructed from a rate matrix on nucleotides.

Thus model describes RNA editing (or lack thereof) at a single site.

Examples

HKY85 +> RNAEdit({})                  # no editting
HKY85 +> RNAEdit({"C":"U"})           # C->U editting