trimNeighbors: Trim Neighbors
In girke-lab/ChemmineR-git-svn-bridge: Cheminformatics Toolkit for R

Description Usage Arguments Value Author(s) See Also Examples

Further reduce the cutoff value of a nearest neighbor (NN) table, as produced by nearestNeighbors. This allows one to compute a very relaxed NN table initially, and then quickly restrict it later without having to re-compute all the similarities.

1	trimNeighbors(nnm, cutoff)

`nnm`	A nearest neighbor table, as produced by `nearestNeighbors`.
`cutoff`	The new similarities cutoff value. All pairs with a similarity less than this value will be removed from the table.

The return value has the same structure as nnm, with some neighbors removed from the indexes and similarties entries.

Kevin Horan

jarvisPatrick nearestNeighbors

   data(sdfsample)
   ap = sdf2ap(sdfsample)
   nnm = nearestNeighbors(ap,numNbrs=20)
   nnm = trimNeighbors(nnm,cutoff=0.5)
   clustering = jarvisPatrick(nnm,k=2,mode="a1b")