check.SamSPECTRAL.input: Checks the input to SamSPECTRAL.

In SamSPECTRAL: Identifies cell population in flow cytometry data.

Description

The input to SamSPECTRAL should be a numeric matrix WITHOUT any NA, NaN, and +/- Inf. This function checks the input matrix and prodeuces an error for an inappropriate input.

Usage

check.SamSPECTRAL.input(data.points,dimensions=1:ncol(data.points),replace.inf.with.extremum=FALSE)

Arguments

data.points	A matrix that contains coordinates of the data points.
dimensions	A vector that determines which dimension of the data point matrix are chosen for investigation.
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 list with the following entries:

data.matrix	The data with infinite elements fixed if replace.inf.with.extremum=TRUE
dimensions	All the checked dimensions.
infinite	Will be TRUE if data contained infinite entries.

Author(s)

Habil Zare

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, Building_Communities, Conductance_Calculation, Connecting

Examples

	## Not run: 
 	   library(SamSPECTRAL)
	
 	  # Reading data file which has been transformed using log transform
 	   data(small_data)
		full <- small
		
 	   checked <- check.SamSPECTRAL.input(data.points=full,dimensions=c(1,2,3),replace.inf.with.extremum=TRUE)
 	   
 	   plot(checked$data.matrix, pch='.')
	
## End(Not run)    

SamSPECTRAL documentation built on Nov. 8, 2020, 5:08 p.m.