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 1.0.3 Index]