translated: Check the sequence type of the pangenome

In FindMyFriends: Microbial Comparative Genomics in R

Description

This method checks whether the genes in the pangenome are on translated form (amino acid sequences) or not. A return value of FALSE only indicates that the storage mode for the genes is not an AAStringSet. While this leaves room for both RNA-, DNA- and BStringSet, only DNAStringSet makes much sense and is therefore assumed

Usage

translated(object)

## S4 method for signature 'pgVirtual'
translated(object)

Arguments

object

A pgVirtual subclass

Value

A boolean indicating whether genes are translated (TRUE) or not (FALSE)

Methods (by class)

• pgVirtual: Sequence type check for pgVirtual subclasses

Examples

testPG <- .loadPgExample()

# Genes are translated
translated(testPG)

# ... and therefore returned as AAStringSet instead of DNAStringSet
class(genes(testPG, subset=1))

FindMyFriends documentation built on Nov. 8, 2020, 6:46 p.m.