FindMyFriends (version 1.2.2)

getRep: Get a representative sequence for each gene group

Description

This method returns a representative sequence for each of the gene groups defined in the pangenome. Currently the methods defined for selecting sequences are 'random', 'shortest', and 'longest. In case of tie for the two latter the first occurence gets returned. Consensus sequence might be added at a latter stage.

Usage

getRep(object, method)
"getRep"(object, method)

Arguments

object

A pgVirtual subclass

method

The method to use to get a representative. Either 'random', 'shortest' or 'longest'.

Value

An XStringSet

Methods (by class)

• object = pgVirtual,method = character: Get a representative sequence for each gene group for pgVirtual subclasses

Examples

testPG <- .loadPgExample(withGroups=TRUE)

# Get a random sequence from each group
getRep(testPG, 'random')