stamLeaf-class {stam}R Documentation

Leaf Nodes in Classifier Nets by StAM

Description

Objects of this class represent leaf nodes in a classifier net as it is used by structured analysis of microarray data. These are the only nodes which have genes annotated.

Objects from the Class

Objects can be created by calls of the form new("stamLeaf", ID, chip, probesidx).

ID
is the GO identifier as character string
chip
the name of the chip for which the classifier net is generated.
probes
a character vector holding the identifiers of the probesets in the order as they occur in the expression matrix

Slots

chip:
Object of class "character", the name of the chip for which the classifier net is generated.
probes:
Object of class "numeric", for each probeset holds its position in the expression metrices to be analyzed
pamfit:
Object of class "nsc", holds the results of pamr.train restricted to the genes annotated to the current leaf node.
delta:
Object of class "numeric", stores the best delty for the local pamfit as determined by pamr.cv.

See stamNode-class fot ID, category, replacedParents and supNode.

Extends

Class "stamNode", directly.

Methods

print
signature(x = "stamLeaf"): print information on the leaf node.
writeHTML
signature(x = "stamLeaf"): generate HTML information on the leaf node.

Author(s)

Claudio Lottaz

See Also

stamNode-class, stamINode-class


[Package stam version 1.0.3 Index]