SMAPProfile-class {SMAP}R Documentation

Class "SMAPProfile"

Description

Holds results from running smap.

Objects from the Class

Objects are not intended to be created directly but as a result from running smap.

Slots

HMM:
Object of class "SMAPHMM"
observations:
Object of class "SMAPObservations"
P:
Object of class "numeric" The log joint posterior probability of the state sequence Q and parameters of HMM given the observations.
Q:
Object of class "numeric" The optimal state sequance (path) in the HMM.
name:
Object of class "character" The name of the object.

Methods

P
signature(object = "SMAPProfile"): Returns the log joint posterior probability.
Q
signature(object = "SMAPProfile"): Returns the optimal state sequence.
HMM
signature(object = "SMAPProfile"): Returns the optimized HMM.
name
signature(object = "SMAPProfile"): Returns the name of the profile.
observations
signature(object = "SMAPProfile"): Returns the observations.
plot
signature(x = "SMAPProfile", y = "missing"): A plot method for the result profile.
[
signature(x = "SMAPProfile"): Creates a new object of class SMAPProfile with extracted elements as specified by the indices provided.

Author(s)

Robin Andersson, robin.andersson@lcb.uu.se

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, SMAPProfiles-class


[Package SMAP version 1.2.0 Index]