gphmm

Generalized Pair Hidden Markov Model (GPHMM)

This package trains a GPHMM and computes GPHMM probabilities.

The model will be described in details in a paper ... coming soon. In the meantime, please don't hesitate to email me if you have questions.

Installation

We are in the process of submitting the package to CRAN. In the meantime, you can install the development version of gphmm from GitHub with the following two lines of code.

library(devtools)
install_github("fperraudeau/gphmm")

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Version

Install

install.packages('gphmm')

Monthly Downloads

Version

0.99.0

License

Artistic-2.0

Maintainer

Fanny Perraudeau

Last Published

October 2nd, 2017

Functions in gphmm (0.99.0)

computeGphmmParam

Compute gphmm parameters from counts.

computegphmm

Compute GPHMM log probability.

generateRandomSequences

Split randomly any R object for which method length() has been defined into a train set and a test set.

generateRead

Generate a noisy read from a true sequence.

calculategphmm

Calculate GPHMM probability.

computeCounts

Compute counts for emissions and transitions.

initializeGphmm

Initial parameters for gphmm.

makeGphmmPerRead

Create a function to compute gphmm probabilities during the training.