stamCV-class {stam} | R Documentation

## Cross Validation Information Generated by StAM

### Description

Objects if this class are generated by `stam.cv`. It contains results of cross validated model fits generated in structured analysis of microarrays in order to choose graph shrinkage levels.

### Objects from the Class

Objects can be created by calls of the form `new("stamCV", exprs, classifications, beta, chip, root)`, but it is recommended the use the function `stam.cv`.

### Slots

`sample.labels`:
  Object of class `"character"`, names of samples
`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
`beta`:
  Object of class `"numeric"`, class weights, one per class
`full.pamfit`:
  Object of class `"nsc"`, PAM fit on all probesets
`probs`:
  Object of class `"array"`, matrix of cross validated prediction probabilities [samples x classes x nodes]
`folds`:
  Object of class `"list"`, buckets used in cross validation
`results`:
  Object of class `"data.frame"`, cross-validated root error rate, root performance and mean redundancy as well as remaining nodes and the accessible probesets for each delta
`node.results`:
  Object of class `"list"`, performance, redundancy, sensitivity and specificity per node
`max.leafdev`:
  Object of class `"numeric"`, performance of worst leaf node
`deltas`:
  Object of class `"numeric"`, shrinkage candidates

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

### Extends

Class `"stamNet"`, directly.

### Methods

print
  `signature(x = "stamCV")`: print information on cross validation
writeHTML
  `signature(x = "stamCV")`: generate HTML information on cross validation. However, using `stam.writeHTML` is recommended.

### Author(s)

Claudio Lottaz

### See Also

`stam.cv`, `stamNet-class`

[Package stam version 1.4.0 Index]