nearestNeighbors: Nearest Neighbors

In girke-lab/ChemmineR: Cheminformatics Toolkit for R

Nearest Neighbors

Description

Computes the nearest neighbors of descriptors in an FPset or APset object for use with the jarvisPatrick clustering function. Only one of numNbrs or cutoff should be given, cutoff will take precedence if both are given. If numNbrs is given, then that many neighbors will be returned for each item in the set. If cutoff is given, then, for each item X, every neighbor that has a similarity value greater than or equal to the cutoff will be returned in the neighbor list for X.

Usage

   nearestNeighbors(x, numNbrs = NULL, cutoff = NULL, ...)

Arguments

x	Either an FPset or an APset.
numNbrs	Number of neighbors to find for each item. If not enough neighbors can be found the matrix will be padded with NA.
cutoff	The minimum similarity value an item must have to another item in order to be included in that items neighbor list. This parameter takes precedence over numNbrs. This parameter allows to obtain tighter clustering results.
...	These parameters will be passed into the distance function used, either cmp.similarity or fpSim, for APset and FPset, respectively.

Value

The return value is a list with the following components:

indexes	index values of nearest neighbors, for each item. If cutoff is used, this will be a list of lists, otherwise it will be a matrix
names	The names of each item in the set, as returned by cid
similarities	The similarity values of each neighbor to the item for that row. This will also be either a list of lists or a matrix, depending on whether or not cutoff was used. Each similarity values corresponds to the id number in the same position in the indexes entry

Author(s)

Kevin Horan

See Also

jarvisPatrick trimNeighbors

Examples

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

girke-lab/ChemmineR documentation built on July 28, 2023, 10:36 a.m.