get_HD_matrices_using_markov: Get a matrix of simulated exchanged hydrogens for each...

In powerHaDeX: Efficient Simulation of HDX-MS Data and Tools for the Statistical Analysis

Get a matrix of simulated exchanged hydrogens for each experiment time point using markov chains

Description

Calculate matrices of simulated exchange required for obtaining empirical distribution.

Usage

get_HD_matrices_using_markov(
  sequence,
  transition_probs,
  steps_between_time_points,
  n_molecules = 100
)

Arguments

sequence	amino acid sequence of a peptide as a character vector
transition_probs	list of probabilities of exchange returned by the get_exchange_probabilities function
steps_between_time_points	A vector containing sum of steps between times at which deuteration levels are measured.
n_molecules	number of peptide molecules

Details

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.

Value

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.

powerHaDeX documentation built on March 18, 2022, 7:40 p.m.