R/AllClasses.R

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

.onLoad <- function(lib, pkg) require("methods", quietly=TRUE)

## Class SMAPObservations
setClass("SMAPObservations",
         representation(## Vector of values (ratios or log2-ratios)
                        value="numeric",
                        ## Vector of chromosomes
                        chromosome="character",
                        ## Vector of unique chromosomes
                        chroms="character",
                        ## Vector of chromosome start positions
                        chrom.start="numeric",
                        ## Vector of start positions
                        startPosition="numeric",
                        ## Vector of end positions
                        endPosition="numeric",
                        ## Optional slots:
                        ## Assay name
                        name="character",
                        ## Vector of reporter ids
                        reporterId="character",
                        ## Derived slots
                        ## Vector of distance between clones
                        distance = "numeric",
                        ## Vector overlapping spots
                        overlapIds="numeric",
                        ## Vector of overlaps
                        overlaps="numeric",
                        ## Vector of start indices for each clone
                        ## in the previous two vectors
                        startOverlaps="numeric",
                        ## Vector of number of overlaps for each clone
                        noOverlaps="numeric",
                        noObservations="numeric"
                        ))

## Class SMAPHMM
setClass("SMAPHMM",
         representation(## Matrix of transition probabilities
                        A="matrix",
                        ## Vector of initial probabilities
                        Pi="numeric",
                        ## List of dparam objects for each distribution
                        Phi="list",
                        ## Length of states vector
                        noStates="numeric",
                        ## Matrix of transition probabilities
                        Z="matrix",
                        ## Vector of initial probabilities
                        Y="numeric",
                        eta="ANY",
                        grad="ANY"
                        ))

## Class SMAPProfile
setClass("SMAPProfile",
         representation(## SMAPHMM
                        HMM="SMAPHMM",
                        ## SMAPObservations
                        observations="SMAPObservations",
                        ## Joint posterior log probability
                        P="numeric",
                        ## State sequence
                        Q="numeric",
                        ## Name
                        name="character"
                        ))

## Class SMAPProfiles
setClass("SMAPProfiles",
         representation(name="character"),
         contains="list")

## Class grad
setClass("grad",
         representation(## Matrix of transition probabilities
                        A="matrix",
                        ## Vector of initial probabilities
                        Pi="numeric",
                        ## List of dparam objects for each distribution
                        Phi="list"
                        ))

## Class eta
setClass("eta",
         representation(value="numeric",
                        ## Matrix of transition probabilities
                        A="matrix",
                        ## Vector of initial probabilities
                        Pi="numeric",
                        ## List of dparam objects for each distribution
                        Phi="list"
                        ))

## Class gaussparam
setClass("gaussparam",
         representation(mean="numeric",
                        sd="numeric"))