lengthWord_probabilities {drimmR}

Probability of occurrence of the observed word of size m in a sequence at several positions

Description

Probability of occurrence of the observed word of size m in a sequence at several positions

Usage

lengthWord_probabilities(m, sequence, pos, x, output_file = NULL, plot = FALSE)

Arguments

m

An integer, the length word

sequence

A vector of characters

pos

A vector of integer positions

x

An object of class dmm

output_file

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

plot

FALSE (default); TRUE (display figure plots of probabilities of occurrence of the observed word of size m by position)

Value

A dataframe of probability by position

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_probability

Examples

data(lambda, package = "drimmR")
length(lambda) <- 1000
dmm <- fitdmm(lambda, 1, 1, c('a','c','g','t'), init.estim = "freq", fit.method="sum")
m <- 2
lengthWord_probabilities(m, lambda, c(1,length(lambda)-m), dmm, plot=TRUE)