This package provides two useful subroutines:
- Given a score threshold
α,score2pvaluecalculates the p-value, i.e. the probability of a set of strings generated from a specfied background model such that each string in this set can attain a score higher than or equal toαwith respect to the inputpwm. - Given a p-value
pval,pval2scorecalculates the highest scoreαsuch thatscore2pvalue(pwm,α)is larger than or equal topval.
By default, the background model is specified as i.i.d discrete uniform.
This is an implementation of:
Efficient and accurate P-value computation for Position Weight Matrices by Touzet et al. https://almob.biomedcentral.com/articles/10.1186/1748-7188-2-15
using MotifPvalue
# An example PWM
pwm = [-2.86995 1.3814 1.36906 -4.88479 -4.19164 -4.88479 1.36607 -5.57793 -0.336375 1.38238;
1.36707 -5.57793 -2.86995 -0.294869 -4.88479 1.34492 -3.49849 1.26497 -2.1768 -4.88479;
-5.57793 -4.47899 -5.57793 1.11923 -3.78584 -5.57793 -4.88479 -5.57793 0.798703 -5.57793;
-4.19164 -5.57793 -4.88479 -1.68576 1.375 -1.88885 -3.17976 -0.798616 -0.0526305 -5.57793];
# Compute pvalue with pwm and score = 4
score2pvalue(pwm, 4)
> 0.000213623046875
# Compute the score-threshold for p-value 1e-4
pvalue2score(pwm, 1e-4)
> 5.57