groupNames: Get and set the names of gene groups in the pangenome

In thomasp85/FindMyFriends: Microbial Comparative Genomics in R

Description

These methods lets you manipulate the naming of gene groups in the pangenome. By default organisms are numbered consecutively but this can be changed at will. New gene groups will be numbered though despite what naming scheme has been introduced before.

Usage

groupNames(object)

groupNames(object) <- value

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

## S4 replacement method for signature 'pgInMem'
groupNames(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 gene group names for pgInMem subclasses

• pgInMem: Set gene group names for pgInMem subclasses

Note

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

Examples

testPG <- .loadPgExample(withGroups=TRUE)
head(groupNames(testPG))

groupNames(testPG)[20] <- 'Gene group 20'

thomasp85/FindMyFriends documentation built on April 25, 2020, 1:06 p.m.