SMAPObservations: Constructor for "SMAPObservations" objects

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

View source: R/methods-SMAPObservations.R

Description

A constructor for SMAPObservations-class objects.

Usage

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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).

Details

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

Value

An object of class SMAPObservations-class.

Author(s)

Robin Andersson, [email protected]

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

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## 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])

SMAP documentation built on Nov. 1, 2018, 5 a.m.