alphabet: Base information for sequence characters of nucleotide...

In Modstrings: Working with modified nucleotide sequences

Description

The alphabet(), shortName() fullName() and nomenclature() functions return the letters, names and associated abbreviations for the type of ModString. alphabet() returns the normal letters and modification letters, whereas shortName(), fullName() and nomenclature() return results for modifications only.

Usage

shortName(x)

fullName(x)

nomenclature(x)

## S4 method for signature 'ModString'
alphabet(x, baseOnly = FALSE)

## S4 method for signature 'ModStringSet'
alphabet(x, baseOnly = FALSE)

## S4 method for signature 'ModString'
shortName(x)

## S4 method for signature 'ModStringSet'
shortName(x)

## S4 method for signature 'ModString'
fullName(x)

## S4 method for signature 'ModStringSet'
fullName(x)

## S4 method for signature 'ModString'
nomenclature(x)

## S4 method for signature 'ModStringSet'
nomenclature(x)

Arguments

x	a ModString or ModStringSet object
baseOnly	TRUE or FALSE (default): Should the result omit occurances of the letters N.-+?

Value

a character vector.

Examples

alphabet(ModDNAString())
shortName(ModDNAString())
nomenclature(ModDNAString())

Modstrings documentation built on Nov. 8, 2020, 7:51 p.m.