SMAPObservations-class {SMAP} | R Documentation |
Holds observed microarray intensity ratios and clone annotations for the SMAP package.
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
.
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.
signature(object = "SMAPObservations")
: Returns
the values of the observations.
signature(object = "SMAPObservations")
:
Returns the chromosome annotations of the observations.
signature(object = "SMAPObservations")
:
Returns the start positions of the observations.
signature(object = "SMAPObservations")
:
Returns the end positions of the observations.
signature(object = "SMAPObservations")
:
Returns the identifiers of the observations.
signature(object = "SMAPObservations")
: Returns
the name of the observation set.
signature(object = "SMAPObservations")
:
Returns the number of observations in the set.
signature(.Object = "SMAPObservations")
:
Creates an instance.
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.
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