FindMyFriends (version 1.2.2)

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

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
"geneNames"(object)
"geneNames"(object) <- value
"geneNames"(object)
"geneNames"(object) <- value
"geneNames"(object)
"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

Examples

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

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