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

Description Usage Arguments Value Methods (by class) Note Examples

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

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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)

Note

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

Examples

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

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

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