getNeighborhood: Extract a graph representation of a gene group neighborhood
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, ...)
"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
testPG <- .loadPgExample(geneLoc=TRUE, withNeighborhoodSplit=TRUE)
# Look at the surroundings of group 10neighborhood <- getNeighborhood(testPG, group=10)