SMAPObservations-class: Class "SMAPObservations": A class to manage microarray
observations for the SMAP package
Description
Holds observed microarray intensity ratios and clone
annotations for the SMAP package.Objects from the Class
Objects can be created by calls of the form
new("SMAPObservations", value, chromosome, startPosition,
endPosition, name, reporterId). Values for internal slots
(see below) are not intended to be passed upon construction.
You can also use the convenience
function SMAPObservations.Slots
value:- Object of class
"numeric" Microarray
intensity ratios. chromosome:- Object of class
"character"
Associated chromosomes for the observations. startPosition:- Object of class
"numeric"
Associated start positions for the observations. endPosition:- Object of class
"numeric"
Associated end positions for the observations. reporterId:- Object of class
"character"
Identifiers of the observations, e.g., probe ids. name:- Object of class
"character" An identifier
of the observation set. noObservations:- Object of class
"numeric" The
number of observations in the set. chrom.start:- Object of class
"numeric".
Internal slot. chroms:- Object of class
"character".
Internal slot. distance:- Object of class
"numeric".
Internal slot. noOverlaps:- Object of class
"numeric".
Internal slot. overlaps:- Object of class
"numeric".
Internal slot. overlapIds:- Object of class
"numeric".
Internal slot. startOverlaps:- Object of class
"numeric".
Internal slot.
Methods
- value
signature(object = "SMAPObservations"): Returns
the values of the observations.- chromosome
signature(object = "SMAPObservations"):
Returns the chromosome annotations of the observations.- startPosition
signature(object = "SMAPObservations"):
Returns the start positions of the observations.- endPosition
signature(object = "SMAPObservations"):
Returns the end positions of the observations.- reporterId
signature(object = "SMAPObservations"):
Returns the identifiers of the observations.- name
signature(object = "SMAPObservations"): Returns
the name of the observation set.- noObservations
signature(object = "SMAPObservations"):
Returns the number of observations in the set.- initialize
signature(.Object = "SMAPObservations"):
Creates an instance.- plot
signature(x = "SMAPObservations", y = "missing"):
A plot method for the observations.- [
signature(x = "SMAPPObservations"): Creates a new
object of class SMAPObservations with extracted elements as
specified by the indices provided.
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