defaults: Access default values for a pgVirtual subclass object

Description Usage Arguments Details Value Methods (by class) Examples

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

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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.

Value

A named list of default values

Methods (by class)

Examples

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

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

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