getNeighborhood: Extract a graph representation of a gene group neighborhood

In FindMyFriends: Microbial Comparative Genomics in R

Description

This method creates a graph representation of the imidiate neighborhood of a gene group. It is different from creating a subgraph of the panchromosome in that only vertices and edges directly reachable from the gene group is included. The vertices will be annotated with a centerGroup property indicating whether or not the node is the queried gene group.

Usage

getNeighborhood(object, ...)

## S4 method for signature 'pgVirtualLoc'
getNeighborhood(object, group, vicinity = 4)

Arguments

object	A pgVirtualLoc subclass
...	Parameters passed on.
group	Either the name or the index of the group whose neighborhood is of interest
vicinity	An integer giving the number of gene groups in both directions to collect

Value

An igraph object with gene groups as vertices and positional connections as edges. The edges is weighted according to the number of genes sharing the connection. All vertices have a centerGroup attribute, which is FALSE for all but the center group.

Methods (by class)

• pgVirtualLoc: Gene group neighborhoods for all pgVirtualLoc subclasses

See Also

plotNeighborhood for nice plotting of the neighborhood

Examples

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

# Look at the surroundings of group 10
neighborhood <- getNeighborhood(testPG, group=10)

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