stam.fit {stam}R Documentation

Fit StAM Model to Training Data

Description

Using the whole expression data provided fit one StAM model according to the chosen shrinkage level.

Usage

stam.fit(cv, expression.matrix, collapse.scnodes = FALSE, 
         alpha = 0.5, delta = NULL, max.nodes = 100)

Arguments

cv result stam.cv on the same data, must be of class stamCV
expression.matrix holds the expression levels. It may be of class exprSet or a plain numeric matrix. In the first case exprs is used to extract the expression levels. The matrix is expected to hold one column per sample and one row per probeset.
collapse.scnodes if set to TRUE replace single children nodes after shrinkage
alpha root performance vs. mean redundancy weight. If set to NULL the root error rate is used exclusively to determine the best shrinkage level. If a numeric vector is provided, all alternatives are computed and the user is given an interactive choice. Values between 0 and 1 are valid, 0 meaning exclusive weight on redundancy and 1 putting exclusive weight on performance.
delta overrule alpha and set shrinkage level explicitely.
max.nodes choose default shrinkage level such that no more than this number of nodes remain after shrinkage.

Details

In a first step stam.fit must choose a shrinkage level. In order to do so it uses results stored in the cv. If the user provides a shrinkage level explicitly this delta is used. If he specifies a single weighting factor alpha the corresponding weighted score is used to determine the best shrinkage level. If alpha is set to a vector of values, the corresponding scores are computed and a default delta is suggested using the median value of the alphas. If this shrinkage level leads to more than max.nodes nodes remaining the shrinkage level is increase until no more than max.nodes remain after shrinkage.

Using the thus determined shrinkage level a weighting of nodes is computed using the leaf node results from cv. Thereby, the whole dataset supplied is used.

Value

An object of class stamFit is returned. You may use the print and plot methods to further investigate the returned value.

Author(s)

Claudio Lottaz

See Also

stam.cv, stamFit-class, plot.stamFit, stam.graph.plot, stam.writeHTML

Examples


# load and prepare some data
golubTrain <- golubNorm[,1:38]
data(golubTrain.cv)

# compute fit
golubTrain.fit <- stam.fit(golubTrain.cv, golubTrain, alpha=seq(0, 1, 0.1))

# investigate
print(golubTrain.fit)
plot(golubTrain.fit)

# show clickable web-page
## Not run: 
map <- stam.graph.plot(golubTrain.fit, outfile="golubTrain")
cat("<HTML><BODY><MAP NAME='graph_map'>", map, "</MAP>",
    "<IMG SRC='golubTrain_graph_plot.png' USEMAP='#graph_map'></BODY></HTML>\n", 
    file="graph_plot.html")
browseURL(paste("file://", getwd(), "/graph_plot.html", sep=""))
## End(Not run)

[Package stam version 1.0.3 Index]