stam.net {stam}R Documentation

Generate a Classifier Graph for StAM

Description

Generates a classifier graph for structured analysis of microarray data based on the Gene Ontology.

Usage

  stam.net(chip = "hgu95av2", root = "GO:0008150", probes = character(0))

Arguments

chip A character string representing the microarray chip from which data has been generated. A meta data packages of the same name is used to obtain the annotation data, namely for the Gene Ontology.
root The identifier of the GO node to be used as the root of the classifier graph. Only successors of this node are considered to generate the graph.
probes The probe names in the order as they occur in the expression matrix. Indeces according to this character array are used to index probes/probesets.

Details

stam.net crawls through the Gene Ontology starting with the root node specified. It collects all successors of the root into a classifier graph according to the parent-children relations defined in the Gene Ontology. Probesets of the microarray chip at hand are attributed to GO nodes according to the Bioconductor annotation meta data package for the chip.

For any node i which has GO annotations AND successors an additional node i' is introduced to the classifier graph. The new node is added as an additional child to i and all probesets annotated to i are moved to i', such that only leaf nodes hold probesets. Nodes which neither themselves nor any of their successors hold probesets are discarded. stam.net also replaces inner nodes with only one child by their successor.

Value

An object of class stamNet is returned. You may use the print method to obtain detailed information about the classifier graph. You may further investigate any element of the 'nodes' list using the print method.

Author(s)

Claudio Lottaz

See Also

stamNet-class, stam.writeHTML

Examples

# load some data
library(golubEsets)
data(golubMerge)
emat <- exprs(golubMerge)

# determine classifier graph for chip "hu6800" on
# biological processes, taking the positions of 
# probesets in Golub's expression matrix into account
net <- stam.net(chip="hu6800", root="GO:0003673", probes=rownames(emat))

# have a look
print(net)
print(net@nodes[[16]])
print(net@nodes$"GO:0007638")

[Package stam version 1.0.3 Index]