Learn R Programming

SMAP (version 1.36.0)

SMAPObservations: Constructor for "SMAPObservations" objects

Description

A constructor for SMAPObservations-class objects.

Usage

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

Arguments

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).

Value

An object of class SMAPObservations-class.

Details

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

References

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

See Also

smap, SMAPObservations-class, SMAPHMM-class

Examples

Run this code
## 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])

Run the code above in your browser using DataLab