hsmm_pred {signalHsmm} | R Documentation |
hsmm_pred class
Description
A single prediction of signalHsmm
.
A stochastic model of signal peptide produced by signalHsmm
.
Details
Always a named list of five elements
-
sp_probability
is a probability of signal peptide presence. -
sp_start
is a start of potential signal peptide (naively 1 aminoacid). -
sp_end
is a position of last amino acid of signal peptide. -
struc
is numeric vector representing predicted structure of input protein. -
prot
is character vector containing input sequence of amino acids. -
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
-
aa_group
encoding of amino acids. Seeaaaggregation
for an example. -
pipar
probabilities of initial state in Markov Model. -
tpmpar
matrix of transition probabilities between states. -
od
matrix of response probabilities. Eg. od[1,2] is a probability of signal 2 in state 1. -
overall_probs_log
probabilities of amino acids in mature protein. -
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