getNeighborhood {FindMyFriends} | R Documentation |
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.
getNeighborhood(object, ...) ## S4 method for signature 'pgVirtualLoc' getNeighborhood(object, group, vicinity = 4)
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 |
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.
pgVirtualLoc
: Gene group neighborhoods for all pgVirtualLoc
subclasses
plotNeighborhood
for nice plotting of the neighborhood
testPG <- .loadPgExample(geneLoc=TRUE, withNeighborhoodSplit=TRUE) # Look at the surroundings of group 10 neighborhood <- getNeighborhood(testPG, group=10)