SMAPProfile-class: Class "SMAPProfile"

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

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, [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, SMAPProfiles-class

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