graphGrouping {FindMyFriends} | R Documentation |
This method takes a similarity matrix based on all genes in the pangenome,
converts it to a graph representation and uses one of igraphs community
detection algorithms to split all genes into groups. Within the FindMyFriends
framework the similarity matrix would usually come from
kmerSimilarity
, but it can just as well be defined in other
ways e.g. be blast derived.
graphGrouping(object, ...) ## S4 method for signature 'pgVirtual' graphGrouping(object, similarity, algorithm, ...)
object |
A pgVirtual subclass |
... |
parameters to be passed on to the community detection algorithm |
similarity |
A similarity matrix with rows and columns corresponding to the genes in the pangenome. |
algorithm |
A string naming the algorithm. See
|
An object of the same class as 'object'.
pgVirtual
: graph grouping for all pgVirtual subclasses
Other grouping algorithms: cdhitGrouping
,
gpcGrouping
, manualGrouping
testPG <- .loadPgExample() # Too heavy to include ## Not run: # Generate similarity matrix simMat <- kmerSimilarity(testPG, lowerLimit=0.75) # Group genes testPG <- graphGrouping(testPG, simMat) ## End(Not run)