eiCluster: Cluster compounds

In girke-lab/eiR: Accelerated similarity searching of small molecules

Cluster compounds

Description

Uses Jarvis-Patrick clustering to cluster the compound database using the LSH algorithm to quickly find nearest neighbors.

Usage

	eiCluster(runId,K,minNbrs,compoundIds=c(), dir=".",cutoff=NULL,
							 distance=getDefaultDist(descriptorType),
							 conn=defaultConn(dir), searchK=-1,type="cluster",linkage="single")

Arguments

runId	The id number identifying a particular set of settings for a database. This is generally the number returned by eiMakeDb. If your coming from an older version of eiR, you should not use this value instead of specifying r, d, and descriptorType.
K	The number of neighbors to consider for each compound.
minNbrs	The minimum number of neighbors that two comopunds must have in common in order to be joined.
compoundIds	If this variable is set to a vector of compound ids, then clustering will be done with just those compounds. If left unset or empty, clustering will apply to all compounds in the given run.
dir	The directory where the "data" directory lives. Defaults to the current directory.
distance	The distance function to be used to compute the distance between two descriptors. A default function is provided for "ap" and "fp" descriptors.
cutoff	Distance cutoff value. Compounds having a distance larger this this value will not be included in the nearest neighbor table. Note that this is a distance value, not a similarity value, as is often used in other ChemmineR functions.
conn	Database connection to use.
searchK	Tunable Annoy LSH parameter. A larger value will give more accurate results, but will take longer time to return. The default value of -1 will allow the value to chosen automatically, which will set a value of numTrees * (approximate number of nearest neighbors). See Annoy page for details. https://github.com/spotify/annoy
type	If "cluster", returns a clustering, else, if "matrix", returns a list in the format expected by the jarvisPatrick function in ChemmineR. This list contains the nearest neighbor matrix along with the similarity matrix. This allows one to quickly try different cutoff values without having to re-compute the whole similarity matrix each time. Note that since we are returning similarity values here instead of distance values, this will only work if the given distance function returns a value between 0 and 1. This is true of the default funtions.
linkage	Can be one of "single", "average", or "complete", for single linkage, average linkage and complete linkage merge requirements, respectively. In the context of Jarvis-Patrick, average linkage means that at least half of the pairs between the clusters under consideration must pass the merge requirement. Similarly, for complete linkage, all pairs must pass the merge requirement. Single linkage is the normal case for Jarvis-Patrick and just means that at least one pair must meet the requirement.

Details

The jarvis patrick clustering algorithm takes a set of items, a distance function, and two parameters, K, and minNbrs. For each item, it find the K nearest neighbors of that item. Normally this requires computing the distance between every pair of items. However, using Locality Sensative Hashing (LSH), the set of nearst neighbors can be found in near constant time. Once the nearest neighbor matrix is computed, the algorithm makes one pass through the items and merges all pairs that have at least minNbrs neighbors in common.

Although not required, it is avisable to specify a cutoff value. This is the maximum distance two items can have from each other and still be considered to be neighbors. It is thus possible for an item to end up with less than K neighbors if less than K items are close enough to it. If a cutoff is not specified, it is possible for highly un-related items to be listed as neighbors of another item simply because nothing else was nearby. This can lead to items being joined into clusters with which they have no true connection.

The type parameter can be used to return a list which can be used to call the jarvisPatrick function in ChemmineR directly. The advantage of this is that it will contain the similarity matrix which can then be used to quickly set different cutoff values (using trimNeighbors) whithout having to re-compute the similarity matrix. Note that this requires that the given distance function return a value between 0 and 1 so it can be converted to a similarity function.

Value

If type is "cluster", returns a clustering. This will be a vector in which the names are the compound names, and the values are the cluster labels. Otherwise, if type is "matrix", returns a list with the following components:

indexes	index values of nearest neighbors, for each item.
names	The database compound id of each item in the set.
similarities	The similarity values of each neighbor to the item for that row. Each similarity values corresponds to the id number in the same position in the indexes entry

If there are not K neibhbors for a compound, that row will be padded with NAs.

Author(s)

Kevin Horan

Examples

	library(snow)
   r<- 50
   d<- 40

   #initialize
   data(sdfsample)
   dir=file.path(tempdir(),"cluster")
   dir.create(dir)
   eiInit(sdfsample,dir=dir,skipPriorities=TRUE)

   #create compound db
   runId=eiMakeDb(r,d,numSamples=20,dir=dir, cl=makeCluster(1,type="SOCK",outfile=""))

	eiCluster(runId,K=5,minNbrs=2,cutoff=0.5,dir=dir)

girke-lab/eiR documentation built on April 19, 2023, 12:52 p.m.