geneNames {FindMyFriends} | R Documentation

## 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

    ## 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'

[Package FindMyFriends version 1.14.0 Index]