nem {MANOR} | R Documentation |
The function nem
computes spatial classification by EM algorithm.
nem.default(LogRatio, Col, Row, nk=nk, beta=1, iters=2000, ...) nem.arrayCGH(arrayCGH, variable, nk=5, beta=1, iters=2000, ...)
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. |
... |
... |
Either a data frame with the following added elements:
ZoneNem |
Vector of label zones. |
ZoneNem |
Vector of label zones. |
People interested in tools for array-CGH analysis can visit our web-page: http://bioinfo.curie.fr.
Philippe Hupé, manor@curie.fr.
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)