pgMatrix

pgMatrix,pgVirtual-method

object


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.


A framework for doing microbial comparative genomics in R.
The main purpose of the package is assisting in the creation of
pangenome matrices where genes from related organisms are
grouped by similarity, as well as the analysis of these data.
FindMyFriends provides many novel approaches to doing pangenome
analysis and supports a gene grouping algorithm that scales
linearly, thus making the creation of huge pangenomes feasible.

Thomas Pedersen

FindMyFriends

Microbial Comparative Genomics in R

pgMatrix function

<ul>
<li> <code>pgVirtual</code>: Get pangenome matrix for pgVirtual subclasses
</li>
</ul>

Methods (by class)

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.

pgMatrix: Get the pangenome matrix

Description

Usage

Arguments

Value

Methods (by class)

Examples