hsmm_pred class

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Description

A single prediction of signalHsmm.

A stochastic model of signal peptide produced by signalHsmm.

Details

Always a named list of five elements

  1. sp_probability is a probability of signal peptide presence.

  2. sp_start is a start of potential signal peptide (naively 1 aminoacid).

  3. sp_end is a position of last amino acid of signal peptide.

  4. struc is numeric vector representing predicted structure of input protein.

  5. prot is character vector containing input sequence of amino acids.

  6. str_approx has value bigger than 0 if the predicted signal peptide structure was approximated (usually in case of sequences that have no signal peptides).

Always a named list of five elements

  1. aa_group encoding of amino acids. See aaaggregation for an example.

  2. pipar probabilities of initial state in Markov Model.

  3. tpmpar matrix of transition probabilities between states.

  4. od matrix of response probabilities. Eg. od[1,2] is a probability of signal 2 in state 1.

  5. overall_probs_log probabilities of amino acids in mature protein.

  6. params matrix of probability distribution for duration. Eg. params[10,2] is probability of duration of time 10 in state 2.

See Also

summary.hsmm_pred plot.hsmm_pred

train_hsmm predict.sighsmm_model