stamFit-class {stam} | R Documentation

## Model Fit Generated by StAM

### Description

Objects of this class hold a model fit as it is generated by structured analysis of microarray data. The function `stam.fit` returns such objects. They are handed on to `stam.predict` for predictions.

### Objects from the Class

Objects can be created by calls of the form `new("stamFit", cv, exprs, alpha, delta, max.nodes, collapse.scnodes)`, but it is recommended to use the function `stam.fit`.

### Slots

`sample.classes`:
  Object of class `"character"`, class names for each sample
`class.labels`:
  Object of class `"character"`, one name for each class
`prior`:
  Object of class `"numeric"`, prior class probabilities according to prevalence
`full.pamfit`:
  Object of class `"nsc"`, PAM fit on all probesets
`alpha`:
  Object of class `"numeric"`, performance vs. redundancy weight(s)
`beta`:
  Object of class `"numeric"`, class weights, one per class
`delta`:
  Object of class `"numeric"`, shrinkage level given by the user
`best.delta`:
  Object of class `"numeric"`, shrinkage level used for computing
`default.delta`:
  Object of class `"numeric"`, default shrinkage level suggested by `stam.fit`
`scores`:
  Object of class `"matrix"`, compound scores weighted using the provided alpha(s)
`alpha.tab`:
  Object of class `"matrix"`, results comparing alphas
`node.results`:
  Object of class `"list"`, performance, redundancy, sensitivity and specificity per node
`collapse.scnodes`:
  Object of class `"logical"`, whether single children nodes are removed after shrinkage

See `stamNet-class` for slots `chip`, `root`, `chippkg`, `GOpkg`, `nodes`, `leafs`, `inodes` and `probes`.

### Extends

Class `"stamNet"`, directly.

### Methods

print
  `signature(x = "stamFit")`: print information on the model fit.
writeHTML
  `signature(x = "stamFit")`: generate HTML information on the model fit, but using `stam.writeHTML` is recommended.

### Author(s)

Claudio Lottaz

### See Also

`stam.fit`, `stamNet-class`

[Package stam version 1.0.3 Index]