trimNeighbors {ChemmineR} | R Documentation

## Trim Neighbors

### Description

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.

### Usage

       trimNeighbors(nnm, cutoff)

### Arguments

`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.

### Value

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

### Author(s)

Kevin Horan

### See Also

`jarvisPatrick` `nearestNeighbors`

### Examples

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

[Package ChemmineR version 3.36.0 Index]