stamFit-class {stam} | R Documentation |
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 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
.
sample.classes
:"character"
, class names for
each sampleclass.labels
:"character"
, one name for each
classprior
:"numeric"
, prior class probabilities
according to prevalencefull.pamfit
:"nsc"
, PAM fit on all probesetsalpha
:"numeric"
, performance vs. redundancy
weight(s)beta
:"numeric"
, class weights, one per classdelta
:"numeric"
, shrinkage level given by the
userbest.delta
:"numeric"
, shrinkage level used for
computingdefault.delta
:"numeric"
, default shrinkage
level suggested by stam.fit
scores
:"matrix"
, compound scores weighted
using the provided alpha(s)alpha.tab
:"matrix"
, results comparing alphasnode.results
:"list"
, performance, redundancy,
sensitivity and specificity per nodecollapse.scnodes
:"logical"
, whether single
children nodes are removed after shrinkage
See stamNet-class
for slots chip
, root
, chippkg
,
GOpkg
, nodes
, leafs
, inodes
and probes
.
Class "stamNet"
, directly.
signature(x = "stamFit")
: print information on the model fit.signature(x = "stamFit")
: generate HTML information on the
model fit, but using stam.writeHTML
is recommended.Claudio Lottaz