geneNames: Get and set the names of the genes in the pangenome

In thomasp85/FindMyFriends: Microbial Comparative Genomics in R

Description

These methods lets you query and change the naming of genes in your pangenome. Take note that even though sequences are not in memory for pgLM objects, the names are. This means that changes to the description header in the underlying fasta files have no effect on the naming in your pangenome

Usage

geneNames(object)

geneNames(object) <- value

## S4 method for signature 'pgLM'
geneNames(object)

## S4 replacement method for signature 'pgLM'
geneNames(object) <- value

## S4 method for signature 'pgFull'
geneNames(object)

## S4 replacement method for signature 'pgFull'
geneNames(object) <- value

## S4 method for signature 'pgSlim'
geneNames(object)

## S4 replacement method for signature 'pgSlim'
geneNames(object) <- value

Arguments

object	A pgVirtual subclass
value	A character vector with new names

Value

In case of the getter, a character vector containing the names of each gene.

Methods (by class)

• pgLM: Get genenames for pgLM and subclasses

• pgLM: Set genenames for pgLM and subclasses

• pgFull: Get genenames for pgFull and subclasses

• pgFull: Set genenames for pgFull and subclasses

• pgSlim: Throws error for pgSlim

• pgSlim: Throws error for pgSlim

Note

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

Examples

testPG <- .loadPgExample()
head(geneNames(testPG))

geneNames(testPG)[10] <- 'Gene number 10'

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