nem {MANOR}R Documentation

Spatial Classification by EM algorithm

Description

The function nem computes spatial classification by EM algorithm.

Usage

## Default S3 method:
nem(LogRatio, Col, Row, nk=nk, beta=1, iters=2000, ...)
## S3 method for class 'arrayCGH':
nem(arrayCGH, variable, nk=5, beta=1, iters=2000, ...)

Arguments

LogRatio Vector that corresponds to the values to be classified.
Col Vector of columns coordinates.
Row Vector of rows coordinates.
nk Integer value corresponding to the number classes.
beta Scale parameter for importance of spatial information.
iters Maximum number of iterations allowed.
arrayCGH Object of class arrayCGH.
variable Variable that corresponds to the values to be classified.
... ...

Value

Either a data frame with the following added elements:

ZoneNem Vector of label zones.
ZoneNem Vector of label zones.

Note

People interested in tools for array-CGH analysis can visit our web-page: http://bioinfo.curie.fr.

Author(s)

Philippe Hupé, manor@curie.fr.

References

C. Ambroise, Approche probabiliste en classification automatique et contraintes de voisinage, Ph.D. thesis, Université de Technologie de Compiègne, 1996.
C. Ambroise, M. Dang, and G. Govaert, Clustering of spatial data by the em algorithm in Geostatistics for Environmental Applications, A. Soares, J. Gomez-Hernandez, and R. Froidevaux, Eds., pp. 493-504. Kluwer Academic Publisher, 1997.
P. Neuvial, P. Hupé, I. Brito, S. Liva, E. Manié, C. Brennetot, A. Aurias, F. Radvanyi, and E. Barillot. Spatial normalization of array-CGH data. In preparation.

Examples

data(spatial)  ## arrays with local spatial effects

## Plot of LogRatio measured on the array CGH
## Not run: 
arrayPlot(edge,"LogRatio", main="Log2-Ratio measured on the array
CGH", zlim=c(-1,1), bar="v", mediancenter=TRUE) 
## End(Not run)

## Spatial trend of the scaled log-ratios (the variable "ScaledLogRatio"
## equals to the log-ratio minus the median value of the corresponding chromosome arm) 
edgeTrend <- arrayTrend(edge, variable="ScaledLogRatio",
span=0.03, degree=1, iterations=3, family="symmetric")

## Not run: 
arrayPlot(edgeTrend, variable="Trend", main="Spatial trend of the array CGH", bar="v") 
## End(Not run)

## Classification with spatial constraint of the spatial trend
edgeNem <- nem(edgeTrend, variable="Trend")
## Not run: 
arrayPlot(edgeNem, variable="ZoneNem", main="Spatial zones identified by nem", bar="v")
## End(Not run)

[Package MANOR version 1.10.0 Index]