
__init__(self,
handle=None)
Read gene expression data from the file handle and return a Record. 
source code



treecluster(self,
transpose=False,
method=' m ' ,
dist=' e ' )
Apply hierarchical clustering and return a Tree object. 
source code



kcluster(self,
nclusters=2,
transpose=False,
npass=1,
method=' a ' ,
dist=' e ' ,
initialid=None)
Apply kmeans or kmedian clustering. 
source code



somcluster(self,
transpose=False,
nxgrid=2,
nygrid=1,
inittau=0.02,
niter=1,
dist=' e ' )
Calculate a selforganizing map on a rectangular grid. 
source code



clustercentroids(self,
clusterid=None,
method=' a ' ,
transpose=False)
Calculate the cluster centroids and return a tuple (cdata, cmask). 
source code



clusterdistance(self,
index1=0,
index2=0,
method=' a ' ,
dist=' e ' ,
transpose=False)
Calculate the distance between two clusters. 
source code





save(self,
jobname,
geneclusters=None,
expclusters=None)
Save the clustering results. 
source code



_savetree(self,
jobname,
tree,
order,
transpose)
Save the hierarchical clustering solution (PRIVATE). 
source code



_savekmeans(self,
filename,
clusterids,
order,
transpose)
Save the kmeans clustering solution (PRIVATE). 
source code



_savedata(self,
jobname,
gid,
aid,
geneindex,
expindex)
Save the clustered data (PRIVATE). 
source code


Inherited from object :
__delattr__ ,
__format__ ,
__getattribute__ ,
__hash__ ,
__new__ ,
__reduce__ ,
__reduce_ex__ ,
__repr__ ,
__setattr__ ,
__sizeof__ ,
__str__ ,
__subclasshook__
