Parameter File Format

The parameters file is evaluated in the python interpreter, so it may cantain any legal python code. In practive it is best to limit the use of this power since it could make the interoperability of parameter files very difficult.

Any assignment in the parameters file is assigned to a variable of the same name in a parameter hash. So, a typical parameter file may look like the following:

transform_method   = "none"
distance_metric    = "euclidean"
cluster_on         = "rows"
agglomerate_method = "clusterNumber"

k = 15
save_intermediate_files = 'yes'

One may insert comments into the parameter file by beginning the line with a '#' character. Also, a convenient shortcut is to use the range() function when specifying an MCCV parameter range.

To activate a meta-wrapper, use the following options,

MCCV = {'on'|'off'}             default to 'off'
Hierarchical = {'on'|'off'}     default to 'off'

If both wrappers are activated, MCCV becomes the inner loop and Hierarchical the outer loop. Be warned, a Hierarchical, MCCV clustering algorithm will take a lot of time and could possibly exhaust your system memory.