ScoringMatrix#
- class lightmotif.ScoringMatrix(values, background=None, *, protein=False)#
A matrix storing position-specific odds-ratio for a motif.
- calculate(sequence)#
Calculate the PSSM score for all positions of the given sequence.
- Returns:
StripedScores– The PSSM scores for every position of the input sequence, stored into a striped matrix for fast vectorized operations.
Note
This method uses the best implementation for the local platform, prefering AVX2 if available.
- pvalue(score, method='meme')#
Translate an absolute score to a P-value for this PSSM.
- reverse_complement()#
Compute the reverse complement of this scoring matrix.
- score(pvalue, method='meme')#
Translate a P-value to an absolute score for this PSSM.