simmzml: Generate simulated mzml data and compounds list

In yufree/mzrtsim: Raw data (mzML) and peaks list simulation for LC/GC-MS based metabolomics data

Generate simulated mzml data and compounds list

Description

Generate simulated mzml data and compounds list

Usage

simmzml(
  db,
  name,
  n = 100,
  inscutoff = 0.05,
  mzrange = c(100, 1000),
  rtrange = c(0, 600),
  ppm = 5,
  mzdigit = 5,
  scanrate = 0.2,
  pwidth = 10,
  baseline = 100,
  baselinesd = 30,
  sn = 100,
  tailingfactor = 1.2,
  compound = NULL,
  rtime = NULL,
  tailingindex = NULL,
  seed = 42,
  unique = FALSE,
  matrix = FALSE,
  matrixmz = NULL
)

Arguments

db	compound database with MS1 data. e.g. hmdbcms or monams1
name	file name of mzml
n	compound numbers from database, if compound is not NULL, n will be compound number, default 100
inscutoff	intensity cutoff for MS1 spectra, default 0.05
mzrange	m/z range for simulation, peaks out of the range will be removed, default c(100,1000)
rtrange	retention time range for simulation, default c(0,600)
ppm	m/z shift in ppm, default 5
mzdigit	m/z digits, default 5
scanrate	time for each full scan, default 0.2 second or 5 spectra per secound
pwidth	peak width for the compound. If it's a single value, simulated peaks' width will use this number as the lambda of Poisson distribution. If it's a numeric vector, it will be used as the peak width for each compounds.
baseline	noise baseline, default 100
baselinesd	standard deviation for noise, default 30
sn	signal to noise ratio of each compound, default 100 for all compounds when baseline is 100
tailingfactor	tailing factor for peaks, larger means larger tailing, default 1.2
compound	numeric compound index in the database for targeted analysis, default NULL
rtime	retention time for the compounds, if NULL, retention time will be simulated. Default NULL
tailingindex	numeric index for tailing compounds, if NULL, all peaks will tailing. Default NULL
seed	Random seed for reproducibility
unique	if TRUE, one compound will have one spectra. Default FALSE
matrix	if TRUE, m/z from experimental data will be used for background m/z simulation.Default FALSE
matrixmz	custom matrix m/z vector, default NULL and predefined list will be used.

Value

one mzML file for simulated data and one csv file the simulated compounds with retention time, m/z and name

Examples

data(monams1)
simmzml(db=monams1, name = 'test')

yufree/mzrtsim documentation built on March 16, 2024, 12:22 p.m.