getNeighborhood: Extract a graph representation of a gene group neighborhood

Description Usage Arguments Value Methods (by class) See Also Examples

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

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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)

See Also

plotNeighborhood for nice plotting of the neighborhood

Examples

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

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

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