word_probability {drimmR}

Probability of a word at a position t of a DMM

Description

Probability of a word at a position t of a DMM

Usage

word_probability(word, pos, x, output_file = NULL, internal = FALSE, ncpu = 2)

Arguments

word

A subsequence (string of characters)

pos

A position (numeric)

x

An object of class dmm

output_file

(Optional) A file containing the probability (e.g,"C:/.../PROB.txt")

internal

FALSE (default) ; TRUE (for internal use of word applications)

ncpu

Default=2. Represents the number of cores used to parallelized computation. If ncpu=-1, then it uses all available cores.

Value

A numeric, probability of word

Author(s)

Victor Mataigne, Alexandre Seiller

References

Barbu VS, Vergne N (2018). “Reliability and survival analysis for drifting Markov models: modelling and estimation.” Methodology and Computing in Applied Probability, 1–33. doi: 10.1007/s11009-018-9682-8, https://doi.org/10.1007/s11009-018-9682-8. Vergne N (2008). “Drifting Markov models with polynomial drift and applications to DNA sequences.” Statistical Applications in Genetics Molecular Biology , 7(1) . doi: 10.2202/1544-6115.1326, https://doi.org/10.2202/1544-6115.1326.

See Also

fitdmm, getTransitionMatrix, word_probabilities, words_probabilities

Examples

data(lambda, package = "drimmR")
dmm <- fitdmm(lambda, 1, 1, c('a','c','g','t'), init.estim = "freq", fit.method="sum")
word_probability("aggctga",4,dmm)