This is a class representation for storing the outputs of the pumaPCA function. Objects of this class should usually only be created through the
Objects from the Class
Objects can be created by calls of the form
Object of class "pumaPCAModel" representing the model parameters
Object of class "pumaPCAExpectations" representing the model expectations
Object of class "matrix" representing the variance in the expression levels
Object of class "matrix" representing the expression levels
Object of class "AnnotatedDataFrame" representing the phenotype information
Object of class "numeric" representing the time it took
Object of class "numeric" representing the number of iterations it took
Object of class "list" representing the history of likelihood values while
Object of class "list" representing the history of how long each iteration took while
Object of class "list" representing the history of how the model was changing while
Object of class "character" representing the reason
pumaPCAhalted. 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"
signature(x="pumaPCARes-class"): plots two principal components on a scatter plot.
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".
Richard D. Pearson
pumaPCA and related class