add_noise_to_one_spectrum: Add noise to a single spectrum

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

Add noise to a single spectrum

Description

This function adds noise to intensities and/or masses in a spectrum.

Usage

add_noise_to_one_spectrum(
  spectrum,
  undeuterated_mass,
  mass_deviations = 50,
  intensity_deviations = NULL
)

Arguments

spectrum	a single spectrum from the list obtained using make_experimental_design.
undeuterated_mass	the value of mass of an undeuterated peptide computed by get_undeuterated_mass.
mass_deviations	mass deviation in parts per million. Either a single number (then the error at each time point will be the same) or a vector of the same length as number of unique time points in the experiment. The error will be sampled from normal distribution with standard deviation equal to mass_deviations * undeuterated_mass/1e6 Default to 50.
intensity_deviations	optional, standard deviations of random noise that will be added to intensities. Either a single number (then the error at each time point will be the same) or a vector of the same length as number of unique time points in the experiment. The error will be sampled from normal distribution with these standard deviations.Default NULL.

Details

The deviations are calculated as follows

sd = mass_deviations * undeuterated_mass/10^6

. To add noise this function uses add_noise_to_one_timepoint and add_noise_to_intensities.

Value

data.table containing a single noisy spectrum

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