pgMatrix: Get the pangenome matrix

In thomasp85/FindMyFriends: Microbial Comparative Genomics in R

Description

This method lets you extract the pangenome matrix of the pangenome. It is not possible to directly change the pangenome matrix as it not necessary stored in the object but might be calculated on request. Either way the pangenome matrix is a function of the gene grouping and should be changed by changing the gene grouping instead of being manipulated downstream.

Usage

pgMatrix(object)

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

Arguments

object

A pgVirtual subclass

Value

A matrix with organisms as columns and gene groups as rows

Methods (by class)

• pgVirtual: Get pangenome matrix for pgVirtual subclasses

Examples

testPG <- .loadPgExample(withGroups=TRUE)

head(pgMatrix(testPG))

thomasp85/FindMyFriends documentation built on April 25, 2020, 1:06 p.m.