SMAPProfile-class: Class "SMAPProfile"

Description Objects from the Class Slots Methods Author(s) References See Also

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, [email protected]

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. 1, 2018, 5 a.m.