SMAPObservations-class: Class "SMAPObservations": A class to manage microarray...

In SMAP: A Segmental Maximum A Posteriori Approach to Array-CGH Copy Number Profiling

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.

Author(s)

Robin Andersson, [e-mail]

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

SMAP documentation built on Nov. 8, 2020, 8:26 p.m.