getRep: Get a representative sequence for each gene group

In FindMyFriends: Microbial Comparative Genomics in R

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)

## S4 method for signature 'pgVirtual,character'
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')

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