FindMyFriends (version 1.2.2)

defaults: 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
"defaults"(object)
"defaults"(object) <- value

Arguments

object

A pgVirtual subclass

value

The new values to set

Value

A named list of default values

Methods (by class)

• pgVirtual: Default values for pgVirtual subclass objects
• pgVirtual: Set defaults for pgVirtual subclass objects

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

Examples

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

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