# A Segmental Maximum A Posteriori Approach to Array-CGH Copy Number Profiling

## Documentation for package ‘SMAP’ version 1.8.0

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

A | Class "SMAPHMM": A class to manage HMMs for the SMAP package
chromosome | Class "SMAPObservations": A class to manage microarray observations for the SMAP package
endPosition | Class "SMAPObservations": A class to manage microarray observations for the SMAP package
GBM | Glioblastoma multiforme array CGH data
HMM | Class "SMAPProfile"
name | Class "SMAPObservations": A class to manage microarray observations for the SMAP package
noObservations | Class "SMAPObservations": A class to manage microarray observations for the SMAP package
noStates | Class "SMAPHMM": A class to manage HMMs for the SMAP package
observations | Class "SMAPProfile"
P | Class "SMAPProfile"
Phi | Class "SMAPHMM": A class to manage HMMs for the SMAP package
Pi | Class "SMAPHMM": A class to manage HMMs for the SMAP package
plot,SMAPObservations,missing-method | Class "SMAPObservations": A class to manage microarray observations for the SMAP package
Q | Class "SMAPProfile"
reporterId | Class "SMAPObservations": A class to manage microarray observations for the SMAP package
smap | smap: A Segmental Maximum A Posteriori Approach to Array-CGH Copy Number Profiling
SMAPHMM | Constructor for "SMAPHMM" objects
SMAPHMM-class | Class "SMAPHMM": A class to manage HMMs for the SMAP package
SMAPObservations | Constructor for "SMAPObservations" objects
SMAPObservations-class | Class "SMAPObservations": A class to manage microarray observations for the SMAP package
SMAPProfile-class | Class "SMAPProfile"
SMAPProfiles-class | Class "SMAPProfiles"
startPosition | Class "SMAPObservations": A class to manage microarray observations for the SMAP package
value | Class "SMAPObservations": A class to manage microarray observations for the SMAP package