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

Creating Motif Numeric Maps

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

Creating Motif Numeric Maps based on motif properties

In the GUI you can create such maps by selecting "Add New ⇒ Motif 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 Motif Numeric Maps based on properties in protocols is the following:

MotifNumericPropertyMap = new Motif Numeric Map(Property: <propertyName> )

Examples

# Create a numeric map based on the size of each motif MotifNumericMap1 = new Motif Numeric Map(Property:Size) # Create a numeric map based on the information content of each motif MotifNumericMap2 = new Motif Numeric Map(Property:IC-length)

Creating Motif Numeric Maps based on motif occurrences

In the GUI you can create such maps by selecting "Add New ⇒ Motif Numeric Map" from the "Data" menu and then go to the "From Track" tab. Select the motif 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 motif in all sequences
Sequence support : returns the number of sequences each motif occurs in
Frequency : returns the motif frequencies (total occurrences of each motif divided by the theoretical maximum number of occurrences)
Max occurrences : the theoretical maximum number of times each motif can occur in the sequences (used to calculate frequency)

The maximum number of potential motif occurrences used to calculate the frequency and max occurrences will depend on both the motif length and the sequence lengths. Hits on both strands are considered, so the frequency for each motif will be: M/(Σ_i 2*(S_i-m+1)), where M is the total number of motif occurrences, m is the motif length and S_i is the sequence length of sequence i. If you want, you can limit the calculations to a subset of the sequences and optionally also only include motifs that lie fully within regions in a second track.

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

MotifOccurrencesMap = new Motif Numeric Map(Track:<motif 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 motif in the TFBS track MotifOccurrences = new Motif Numeric Map(Track:TFBS, property=Total count) # Create a numeric map based on the number of sequences that contain an occurrence of the motif within a repeat region MotifOccurrences = new Motif Numeric Map(Track:TFBS, property=Sequence support, within=RepeatMasker) # Create a numeric map with the frequency of each motif within sequences in the Downregulated collection MotifOccurrences = new Motif Numeric Map(Track:TFBS, property=Frequency, Sequence Collection=Downregulated)