pcGraph

pcGraph,pgVirtualLoc-method

object

Should the returned graph be stripped of all metadata and only
capture gene group connectivity. Defaults to FALSE

slim


This method creates a graph representation of the panchromosome - The 
complete set of gene groups linked together by chromosomal position. Each 
vertice in the graph represent a gene group and each edge represent a 
positional relation between two gene groups (neighboring each other). 
Vertices are annotated with number of genes, organism names and strand while
edges are annotated with numer of genes (as weight), and organism names.


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

pcGraph function

<ul>
<li> <code>pgVirtualLoc</code>: Panchromosome creation for all pgVirtualLoc subclasses
</li>
</ul>

Methods (by class)

This method creates a graph representation of the panchromosome - The 
complete set of gene groups linked together by chromosomal position. Each 
vertice in the graph represent a gene group and each edge represent a 
positional relation between two gene groups (neighboring each other). 
Vertices are annotated with number of genes, organism names and strand while
edges are annotated with numer of genes (as weight), and organism names.

pcGraph: Calculate the panchromosome graph

Description

Usage

Arguments

Value

Methods (by class)

Examples