Difference between revisions of "Matrix (element type)"
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Matrix element type represents a [[wikipedia:Position-specific scoring matrix|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). | Matrix element type represents a [[wikipedia:Position-specific scoring matrix|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 | + | Matrices can only reside inside {{Type link|matrix library}}. Some analyses like [[ChIPMunk (analysis)|ChIPMunk]] or [[Create weight matrix model (analysis)|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 | + | 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 {{Type link|site model}}s. |
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]]. | 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]]. |
Revision as of 16:32, 17 May 2013
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 library. 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.