pumaPCARes-class {puma} | R Documentation

## 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".

### Author(s)

Richard D. Pearson

### See Also

Related method `pumaPCA` and related class `pumaPCARes`.

[Package puma version 3.22.0 Index]