pgMatrix: Get the pangenome matrix

Description Usage Arguments Value Methods (by class) Examples

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

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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

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testPG <- .loadPgExample(withGroups=TRUE)

head(pgMatrix(testPG))


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