Matrix (element type)

An example of weight matrix description in the information box

Title

matrix

Class

FrequencyMatrix

Matrix element type represents a position weight matrix (PWM) which describes some motif. Number of matrix rows depends on the alphabet used (usually 4 rows for mononucleotide alphabet and 16 rows for dinucleotide alphabet).

Matrices can only reside inside matrix libraries. Some analyses like ChIPMunk or Create weight matrix model may produce new matrices.

Matrices themselves do not have any thresholds to predict whether the binding element (transcription factor) binds with given location or not. For this purpose you should use site models.

Matrices cannot be opened as documents. However when you select the matrix in the tree, you can read the comprehend description in the information box.