A Module Numeric Map is a data object that associates modules with numeric values. It is a subtype of Numeric Map which again is a subtype of Map.

Creating Module Numeric Maps

Module Numeric Maps can be created by explicitly assigning values to named modules, module collections, module partition clusters or module ranges. (See documentation under Maps and Numeric Maps). In addition, Module Numeric Maps can be created based on numeric properties of modules or on module occurrences in a module track as described below.

Creating Module Numeric Maps based on module properties

In the GUI you can create such maps by selecting "Add New ⇒ Module Numeric Map" from the "Data" menu and then go to the "From Property" tab and select the property from the drop-down menu. All numeric properties can be selected, both standard and user-defined.

The general syntax for creating Module Numeric Maps based on properties in protocols is the following:

ModuleNumericPropertyMap = new Module Numeric Map(Property: <propertyName> )

Examples

# Create a numeric map based on the number of component motifs in each module ModuleNumericMap1 = new Module Numeric Map(Property:Cardinality) # Create a numeric map based on the sum of the IC-contents for the motif models # having the highest IC for each component motif ModuleNumericMap2 = new Module Numeric Map(Property:Max IC)

Creating Module Numeric Maps based on module occurrences

In the GUI you can create such maps by selecting "Add New ⇒ Module Numeric Map" from the "Data" menu and then go to the "From Track" tab. Select the module track in the top-most drop-down menu and the statistical function from the "Property" menu. Available statistical functions are:

Total count : returns the total number of occurrences for each module in all sequences
Sequence support : returns the number of sequences each module occurs in

If you want, you can limit the calculations to a subset of the sequences and optionally also only include modules that lie fully within regions in a second track.

The general syntax for creating Module Numeric Maps based on module occurrences in a module track is the following:

ModuleOccurrencesMap = new Module Numeric Map(Track:<module track name>, property=<statistical function> , Sequence Collection=<subset>, within=<region dataset> )

Examples

# Create a numeric map based on the total number of occurrences of each module in the CRM track ModuleOccurrences = new Module Numeric Map(Track:CRM, property=Total count) # Create a numeric map based on the number of sequences that contain an occurrence of the module within a repeat region ModuleOccurrences = new Module Numeric Map(Track:CRM, property=Sequence support, within=RepeatMasker)