SMAPObservations: Constructor for "SMAPObservations" objects
In SMAP: A Segmental Maximum A Posteriori Approach to Array-CGH Copy Number Profiling

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/methods-SMAPObservations.R

A constructor for SMAPObservations-class objects.

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SMAPObservations(value, chromosome, startPosition, endPosition,
                 name=character(0),
                 reporterId=as.character(1:length(value)))

`value`	A vector of microarray intensity ratios (numeric).
`chromosome`	A vector of chromosome annotations (character).
`startPosition`	A vector of start positions (numeric).
`endPosition`	A vector of end positions (numeric).
`name`	The name of the observation set (character).
`reporterId`	A vector of observation identifiers, e.g., probe ids (character).

The vectors value, chromosome, startPosition, endPosition, and reporterId must be of equal length.

An object of class SMAPObservations-class.

Robin Andersson, robin.andersson@lcb.uu.se

Andersson, R., Bruder, C. E. G., Piotrowski, A., Menzel, U., Nord, H., Sandgren, J., Hvidsten, T. R., Diaz de Stahl, T., Dumanski, J. P., Komorowski, J., A Segmental Maximum A Posteriori Approach to Array-CGH Copy Number Profiling, submitted

smap, SMAPObservations-class, SMAPHMM-class

## Load Glioblastoma multiforme data
data(GBM)
observations <- SMAPObservations(value=as.numeric(GBM[,2]),
                                 chromosome=as.character(GBM[,3]),
                                 startPosition=as.numeric(GBM[,4]),
                                 endPosition=as.numeric(GBM[,5]),
                                 name="G24460",
                                 reporterId=as.character(GBM[,1]))
## plot observations
plot(observations, ylim=c(0,2))
## plot subset of observations (chromosome 9)
ids <- which(chromosome(observations) == "9")
plot(observations[ids])