MotifPvalue

pval2score(pwm, pval, ϵ=1e-1, k=10, bg=[.25,.25,.25,.25])

Returns the highest score(M,pval) of a pwm such that p-value is greater or equal to pval.

Input:

• pwm: a 4 x m matrix
• pval: a p-value; e.g. pval = 1e-3
• ϵ: initial granularity (optional)
• k: Refinement parameter (optional)
• bg: multinomial background (optional)

Output

• α: the highest score-threshold

score2pvalue(pwm, α, ϵ=1e-1, k=100, bg=[.25,.25,.25,.25])

Returns P-value(M,α) of a pwm with a given threshold α.

Input:

• pwm: a 4 x m matrix
• α: the score
• ϵ: initial granularity (optional)
• k: Refinement parameter (optional)
• bg: multinomial background (optional)

Output:

• pval: p-value