SMAPProfile-class: 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.
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