pcGraph: Calculate the panchromosome graph

In FindMyFriends: Microbial Comparative Genomics in R

Description

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.

Usage

pcGraph(object, ...)

## S4 method for signature 'pgVirtualLoc'
pcGraph(object, slim = FALSE)

Arguments

object	A pgVirtualLoc subclass
...	parameters passed on
slim	Should the returned graph be stripped of all metadata and only capture gene group connectivity. Defaults to FALSE

Value

An igraph object

Methods (by class)

• pgVirtualLoc: Panchromosome creation for all pgVirtualLoc subclasses

Examples

testPG <- .loadPgExample(geneLoc=TRUE, withNeighborhoodSplit=TRUE)

panchromosome <- pcGraph(testPG)

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