variableRegions: Detect regions of high variability in the panchromosome

In thomasp85/FindMyFriends: Microbial Comparative Genomics in R

Description

This method analyses the panchromosome and detects regions of local non-linearity. These regions often corresponds to areas with insertion/deletions, frameshifts or general high plasticity. It works by examining each vertice of the panchromosome with an out degree above 2 and detect cycles within the neighborhood of these vertices. Adjacent cycles are then joined together to form bigger groups of high variability.

Usage

variableRegions(object, ...)

## S4 method for signature 'pgVirtualLoc'
variableRegions(object, flankSize)

Arguments

object	A pgVirtualLoc subclass
...	parameters to pass on
flankSize	The size of the neighborhood around vertices with outdegree above 2 in where to search for cycles

Value

A list of variable regions. Each element contains the following elements:

type

Either 'ins/den', 'frameshift', 'hub', 'plastic' or 'end'. ins/del are regions where the two outgoing vertices are directly connected. frameshift are regions where the two outgoing vertices are connected through two different routes, but not directly. hub are regions with more than two outgoing vertices. plastic are regions where the two outgoing vertices are connected through multiple different paths. end are regions with only one outgoing vertice.

members

The gene groups being part of the region.

flank

The outgoing vertices connecting the region to the rest of the panchromosome.

connectsTo

The gene group(s) each flank connects to outside of the region

graph

The subgraph of the panchromosome representing the region

Methods (by class)

• pgVirtualLoc: Variable region detection for all pgVirtualLoc subclasses

Examples

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

# Too heavy to include
## Not run: 
regions <- variableRegions(testPG)

# Have a look at the first region
regions[[1]]

## End(Not run)

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