Trees  Indices  Help 



object +  Record
Store gene expression data.
A Record stores the gene expression data and related information contained in a data file following the file format defined for Michael Eisen's Cluster/TreeView program.






















Inherited from 


Inherited from 

Read gene expression data from the file handle and return a Record. The file should be in the format defined for Michael Eisen's Cluster/TreeView program.

Apply hierarchical clustering and return a Tree object. The pairwise single, complete, centroid, and average linkage hierarchical clustering methods are available.
See the description of the Tree class for more information about the Tree object returned by this method. 
Apply kmeans or kmedian clustering. This method returns a tuple (clusterid, error, nfound).

Calculate a selforganizing map on a rectangular grid. The somcluster method returns a tuple (clusterid, celldata).

Calculate the cluster centroids and return a tuple (cdata, cmask). The centroid is defined as either the mean or the median over all elements for each dimension.

Calculate the distance between two clusters.

Calculate the distance matrix and return it as a list of arrays.
Return value: The distance matrix is returned as a list of 1D arrays containing the distance matrix between the gene expression data. The number of columns in each row is equal to the row number. Hence, the first row has zero elements. An example of the return value is: matrix = [[], array([1.]), array([7., 3.]), array([4., 2., 6.])] This corresponds to the distance matrix: [0., 1., 7., 4.] [1., 0., 3., 2.] [7., 3., 0., 6.] [4., 2., 6., 0.] 
Save the clustering results. The saved files follow the convention for the Java TreeView program, which can therefore be used to view the clustering result.

Trees  Indices  Help 


Generated by Epydoc 3.0.1 on Mon Jul 10 15:14:24 2017  http://epydoc.sourceforge.net 