defaults {FindMyFriends} | R Documentation

## Access default values for a pgVirtual subclass object

### Description

This method lets the user view and set the default values used for the different algorithms in FindMyFriends. Many of the parameters are reoccuring and it can become laborious to type them in at each step. These functionalities makes it easy to set defaults on a per-pangenome basis.

### Usage

    defaults(object)

    defaults(object) <- value

    ## S4 method for signature 'pgVirtual'
    defaults(object)

    ## S4 replacement method for signature 'pgVirtual'
    defaults(object) <- value

### Arguments

`object` | A pgVirtual subclass
`value` | The new values to set

### Details

Currently the following methods support reading defaults from a pgVirtual object. Note that only directly named arguments are supported - arguments passed on through the `...`-mechanism are not supported unless they are passed to a function that support it.

- `graphGrouping`

- `gpcGrouping`

- `variableRegions`

- `plotGroup`

- `kmerLink`

- `plotSimilarity`

- `plotTree`

- `kmerSimilarity`

### Value

A named list of default values

### Methods (by class)

- `pgVirtual`: Default values for pgVirtual subclass objects

- `pgVirtual`: Set defaults for pgVirtual subclass objects

### Examples

    # Get all object defaults
    testPG <- .loadPgExample()
    defaults(testPG)

    # Set a new default
    defaults(testPG)$minFlank <- 2

[Package FindMyFriends version 1.16.0 Index]