Calculate matrices of simulated exchange required for obtaining empirical distribution.
get_HD_matrices_using_markov(
sequence,
transition_probs,
steps_between_time_points,
n_molecules = 100
)amino acid sequence of a peptide as a character vector
list of probabilities of exchange returned by the
get_exchange_probabilities function
A vector containing sum of steps between times at which deuteration levels are measured.
number of peptide molecules
Matrices are stored in a list of matrices (HD_matrices) -
each matrix for the respective time point of the measurement times.
Using the distributions of process in given times of mesurements, states
H or D are sampled for m peptide molecules
(n_molecules) for each of \(i = 1,..., n\) amino acids and stored
in a m x n dimensional matrix for each of the time points of the
measurement given by times.
The improvement is based on the observation that the considered
process is a Markov chain with transition probabilities \(P(H -> D)\) and
\(P(D -> H)\), and states H and D.