nem: Spatial Classification by EM algorithm

In MANOR: CGH Micro-Array NORmalization

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.

or an object of class arrayCGH with the following elements added to the data.frame attribute arrayValues:

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 Hup?, [e-mail].

References

C. Ambroise, Approche probabiliste en classification automatique et contraintes de voisinage, Ph.D. thesis, Universit? de Technologie de Compi?gne, 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. Hup?, I. Brito, S. Liva, E. Mani?, C. Brennetot, A. Aurias, F. Radvanyi, and E. Barillot. Spatial normalization of array-CGH data. BMC Bioinformatics, 7(1):264. May 2006.

Examples

data(spatial)  ## arrays with local spatial effects

## Plot of LogRatio measured on the array CGH
## Not run: 
GLAD::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: 
GLAD::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: 
GLAD::arrayPlot(edgeNem, variable="ZoneNem", main="Spatial zones identified by nem", bar="v")

## End(Not run)

MANOR documentation built on Nov. 8, 2020, 6:52 p.m.