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

In hadexversum/powerHDX: Efficient Simulation of HDX-MS Data and Tools for the Statistical Analysis

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

Description

Calculate matrices of simulated exchange required for obtaining empirical distribution.

Usage

get_HD_matrices(
  sequence,
  transition_probs,
  experiment_times,
  times_to_record,
  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
experiment_times	numeric vector of times at which exchange will happen
times_to_record	numeric vector of times for which deuteration level measurement should be made
n_molecules	number of peptide molecules

Details

At each time point in the time sequence:

change H to D with probability P(H -> D) in each entry of the matrix from the previous iteration,

change D to H with probability P(D -> H) in each entry of the matrix from the previous iteration.

Value

Matrices are stored in a list of matrices (HD_matrices) - each matrix for the respective time point of the measurement times.

hadexversum/powerHDX documentation built on Aug. 31, 2022, 7:47 p.m.