pumaPCARes-class: Class pumaPCARes
Description
This is a class representation for storing the outputs of the pumaPCA function. Objects of this class should usually only be created through the pumaPCA function.
Objects from the Class
Objects can be created by calls of the form new("pumaPCARes", ...).Slots
model:- Object of class "pumaPCAModel" representing the model parameters
expectations:- Object of class "pumaPCAExpectations" representing the model expectations
varY:- Object of class "matrix" representing the variance in the expression levels
Y:- Object of class "matrix" representing the expression levels
phenoData:- Object of class "AnnotatedDataFrame" representing the phenotype information
timeToCompute:- Object of class "numeric" representing the time it took
pumaPCA to run numberOfIterations:- Object of class "numeric" representing the number of iterations it took
pumaPCA to converge likelihoodHistory:- Object of class "list" representing the history of likelihood values while
pumaPCA was running timingHistory:- Object of class "list" representing the history of how long each iteration took while
pumaPCA was running modelHistory:- Object of class "list" representing the history of how the model was changing while
pumaPCA was running exitReason:- Object of class "character" representing the reason
pumaPCA halted. Can take the values "Update of Likelihood less than tolerance x", "Update of W less than tolerance x", "Iterations exceeded", "User interrupt", "unknown exit reason"
Methods
- plot
signature(x="pumaPCARes-class"): plots two principal components on a scatter plot.- write.reslts
signature(x = "pumaPCARes-class"): writes the principal components for each array to a file. It takes the same arguments as write.table. The argument "file" does not need to set any extension. The file name and extension "csv" will be added automatically. The default file name is "tmp".