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]