Building_Communities {SamSPECTRAL}R Documentation

Builds the communities from the set of all data points.

Description

Some sample points are picked up and the points close to each sample point are considered as members of that community.

Usage

Building_Communities(full, m=3000, space.length=1, community.weakness.threshold=1, talk=TRUE, do.sampling=TRUE,
			   replace.inf.with.extremum=TRUE)

Arguments

full

The matrix containing the coordinates of all data points.

m

An integer determining upper and lower bounds on the final number of sample points which will be in range .95*m/2 and 2 1.1*m

space.length

An estimate for the length of a cube that is assumed to contain all data points.

community.weakness.threshold

The communities with number of members less than this threshold will be ignored. Normally, setting it to 1 is reasonable.

talk

A boolean flag with default value TRUE. Setting it to FALSE will keep running the procedure quite with no messages.

do.sampling

A boolean flag with default value TRUE. If set to FALSE, the sampling stage will be ignored by picking up all the data points.

replace.inf.with.extremum

If TRUE, the Inf and -Inf values will be replaced by maximum and minimum of data in each direction.

Value

Returns a society which is a list of communities.

Author(s)

Habil Zare and Parisa Shooshtari

References

Zare, H. and Shooshtari, P. and Gupta, A. and Brinkman R.B: Data Reduction for Spectral Clustering to Analyse High Throughput Flow Cytometry Data. BMC Bioinformatics, 2010, 11:403.

See Also

SamSPECTRAL,check.SamSPECTRAL.input

Examples

	
	 ## Not run: 
	    library(SamSPECTRAL)

	   # Reading data file which has been transformed using log transform
	    data(small_data)
		full <- small
	
		# Parameters:
		m <- 3000; ns <- 200; sl <- 3; cwt <-1
	
    	# Sample the data and build the communities
    	society <- Building_Communities(full=full,m=m, space.length=sl, community.weakness.threshold=cwt)
	
		# Ploting the representatives:
		plot(full[society$representatives,])

	
## End(Not run)

[Package SamSPECTRAL version 1.48.0 Index]