Generalized Pair Hidden Markov Chain Model for Sequence Alignment


[Up] [Top]

Documentation for package ‘gphmm’ version 0.99.0

Help Pages

calculategphmm Calculate GPHMM probability.
computeCounts Compute counts for emissions and transitions.
computegphmm Compute GPHMM log probability.
computeGphmmParam Compute gphmm parameters from counts.
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.
initializeGphmm Initial parameters for gphmm.
makeGphmmPerRead Create a function to compute gphmm probabilities during the training.