simSpectra: Simulate a mass spectrum

In kuwisdelu/MSExample: An example R package for mass spectrometry

Description

Simulate a mass spectrum including peaks, noise, a baseline, noise, mass drift, mass resolution, etc.

Usage

simSpectra(n = 1L, peaks = 50L, mz = rlnorm(peaks, 7, 0.3),
  intensity = rlnorm(peaks, 1, 0.9), from = 0.9 * min(mz), to = 1.1 *
  max(mz), by = 100, sdpeaks = sdpeakmult * log1p(intensity),
  sdpeakmult = 0.2, sdnoise = 0.1, sdmz = 10, resolution = 1000,
  fmax = 0.5, baseline = 0, decay = 10, units = c("ppm", "mz"),
  representation = c("profile", "centroid"))

Arguments

n	The number of spectra to simulate
peaks	The number of peaks to simulate
mz	The m/z of the peaks
intensity	The intensity of the peaks
from	Lower end of mass range
to	Upper end of mass range
by	Size of m/z bins
sdpeaks	Log-standard deviation of peak intensities
sdpeakmult	Multiplier for peak variance
sdnoise	Standard deviation of noise
sdmz	Mass error
resolution	Mass resolution as defined by 'm / dm' where 'm' is the observed mass and 'dm' is the width of the peak at a proportion of its maximum height defined by fmax (defaults to FWHM)
fmax	The proportion of the maximum peak height used by resolution
baseline	Maximum intensity of hte baseline
decay	Rate of decay of the baseline
units	Units for the width of the m/z bins
representation	Return a profile or centroided spectrum?

Value

A MassSpectrum or MassSpectraList

kuwisdelu/MSExample documentation built on May 13, 2020, 10:25 p.m.