wrappers {clusterCons} | R Documentation |
Functions to wrap command calls to clustering functions
Description
These are primarily internal functions called by cluscomp
to execute
clustering runs and are unlikely to be used directly. The wrappers are detailed in
the algorithm.R
file of the clusterCons
package and the user can add
their own wrappers to this to extend the number of algorithms supported. These five
wrappers allow the user to specify the conditions under which the corresponding
clustering algorithms are run and follow exactly the same specifications as the
corresponding cluster
functions (see agnes
, pam
,
hclust
, diana
and kmeans
).
Usage
agnes_clmem(x, clnum, params = list())
pam_clmem(x, clnum, params = list())
hclust_clmem(x, clnum, params = list())
diana_clmem(x, clnum, params = list())
kmeans_clmem(x, clnum, params = list())
apcluster_clmem(x,clnum,params = list())
Arguments
x |
A data.frame of numerical values to be clustered which must pass the |
clnum |
The number of specified clusters. When using the |
params |
A list of key, value pairs specifying the parameters to pass to the clustering algorithm. These
follow the exact specification of the original functions in the |
Value
Returns a data.frame with row.names matching that of the data.
cm |
cluster membership identifier specifying the cluster into which the row has been classified |
Author(s)
Dr. T. Ian Simpson ian.simpson@ed.ac.uk
References
Merged consensus clustering to assess and improve class discovery with microarray data. Simpson TI, Armstrong JD and Jarman AP. BMC Bioinformatics 2010, 11:590.
See Also
cluster
, agnes
, pam
, hclust
, diana
, kmeans
and apclusterK
Examples
#load some data
data(sim_profile);
#run a basic agnes clustering with 3 clusters
cm <- agnes_clmem(sim_profile,3);
#pass some more complex parameters
agnes_params = list(metric='manhattan',method='single');
cm <- agnes_clmem(sim_profile, 3,params=agnes_params);