orgNames: Get and set the names of organisms in the pangenome

In FindMyFriends: Microbial Comparative Genomics in R

Description

These methods lets you manipulate the naming of organisms in the pangenome. By default organisms are named after the fasta file they are defined by, but this can be changed at will.

Usage

orgNames(object)

orgNames(object) <- value

## S4 method for signature 'pgInMem'
orgNames(object)

## S4 replacement method for signature 'pgInMem'
orgNames(object) <- value

Arguments

object	A pgVirtual subclass
value	A vector with new names - will be coerced to characters

Value

In case of the getter a character vector with names

Methods (by class)

• pgInMem: Get organism names for pgInMem subclasses

• pgInMem: Set organism names for pgInMem subclasses

Note

Required for subclasses of pgVirtual in order to extend the class system of FindMyFriends

Examples

testPG <- .loadPgExample()
orgNames(testPG)

orgNames(testPG)[3] <- 'Organism 3'

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