| stam.fit {stam} | R Documentation |
Using the whole expression data provided fit one StAM model according to the chosen shrinkage level.
stam.fit(cv, expression.matrix, collapse.scnodes = FALSE,
alpha = 0.5, delta = NULL, max.nodes = 100)
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 ExpressionSet, 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. |
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.
An object of class stamFit is returned. You may use the print and plot methods to further investigate the returned value.
Claudio Lottaz
stam.cv, stamFit-class, plot.stamFit,
stam.graph.plot, stam.writeHTML
## Not run:
# prepare data
library(golubEsets)
data(Golub_Merge)
# load and prepare some data
golubTrain <- Golub_Merge[,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)
## End(Not run)
# 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)