exact_mc: Exact method for p-value [Markov chains]

In localScore: Package for Sequence Analysis by Local Score

Exact method for p-value [Markov chains]

Description

Calculates the exact p-value for short numerical Markov chains. Time computation can be too large for a sequence length of several thousands, specially for a data set.

Usage

exact_mc(m, localScore, sequence_length, sequence_min, sequence_max)

Arguments

m	Transition matrix [matrix object]
localScore	score for which the p-value should be calculated
sequence_length	length of the sequence
sequence_min	minimum score
sequence_max	maximum score

Value

A double representing the probability of a localScore as high as the one given as argument

Examples

matrix = t(matrix(c(0.2, 0.3, 0.5, 0.3, 0.4, 0.3, 0.2, 0.4, 0.4), nrow = 3))
exact_mc(localScore = 12, m = matrix, sequence_length = 100, sequence_min = -1, sequence_max = 1)
exact_mc(localScore = 150, m = matrix, sequence_length = 1000, sequence_min = -1, sequence_max = 1)

localScore documentation built on May 17, 2022, 5:09 p.m.