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 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`

# 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]