Generate simulated mzml data and compounds list

simmzml(
  db,
  name,
  n = 100,
  inscutoff = 0.05,
  mzrange = c(100, 1000),
  rtrange = c(0, 600),
  ppm = 5,
  sampleppm = 5,
  mzdigit = 5,
  noisesd = 0.5,
  scanrate = 0.2,
  pwidth = 10,
  baseline = 100,
  baselinesd = 30,
  SNR = 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 for input compounds, default 5
sampleppm: m/z shift in ppm within one sample, default 5
mzdigit: m/z digits, default 5
noisesd: standard deviation for normal distribution of m/z shift, default 0.5
scanrate: time for each full scan, default 0.2 second or 5 spectra per second
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
SNR: 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 from serum blank 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')
#> Warning: mzR has been built against a different Rcpp version (1.0.12)
#> than is installed on your system (1.0.13). This might lead to errors
#> when loading mzR. If you encounter such issues, please send a report,
#> including the output of sessionInfo() to the Bioc support forum at 
#> https://support.bioconductor.org/. For details see also
#> https://github.com/sneumann/mzR/wiki/mzR-Rcpp-compiler-linker-issue.