Heuristic selection of prototypes
Dimensionality reduction of feature vectors
number of prototypes or maximum number of clusters
method to select prototypes or to perform subset selection
data matrix (l x d) of feature vectors (l = number of genes)
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The following heuristics to perform automatic selection of prototypes are implemented:
select n genes with highest number of GO annotations in the currently selected ontology
select n genes uniform randomly over all genes with annotations in the currently selected ontology
To perfom dimensionality reduction implemented methods are:
dimensionality reduction via principal component analysis; the number of principal components is determined such that at least 95% of total variance in feature space can be explained
EM-clustering in feature space
If the function is called to automatically select prototypes, a character vector of gene IDs is returned.
If the function is called to perform dimensionality via PCA, the result is a list with items
If the function is called to perform clustering in feature space, the cluster centers are returned in a l x k matrix (each column is one cluster center). The "flexmix" function in the package "flexmix" is called to perform the clustering. The BIC is used to calculate the optimal number of clusters in the range 2,...,n.
The result depends on the currently set ontology ("BP","MF","CC").
 H. Froehlich, N. Speer, C. Spieth, and A. Zell, Kernel Based Functional Gene Grouping, Proc. Int. Joint Conf. on Neural Networks (IJCNN), pp. 6886 - 6891, 2006
 N. Speer, H. Froehlich, A. Zell, Functional Grouping of Genes Using Spectral Clustering and Gene Ontology, Proc. Int. Joint Conf. on Neural Networks (IJCNN), pp. 298 - 303, 2005
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# takes too much time in the R CMD check proto=selectPrototypes(n=5) # --> returns a character vector of 5 genes with the highest number of annotations feat=getGeneFeaturesPrototypes(c("207","7494"),prototypes=proto,pca=FALSE) # --> compute feature vectors selectPrototypes(data=feat$features,method="pca") # ... and PCA projection
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