simmzml | R Documentation |
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,
pheight = 10,
baseline = 100,
baselinesd = 30,
rf = 100,
tailingfactor = 1.2,
compound = NULL,
rtime = NULL,
tailingindex = NULL,
seed = 42,
unique = FALSE,
matrix = FALSE,
matrixmz = NULL
)
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 peak width for all compounds. If it's a numeric vector, it will be used as the peak widths for every compounds. |
pheight |
peak height for the compound. If it's a single value, simulated peaks' height will use this number as peak height for all compounds. If it's a numeric vector, it will be used as the peak heights for every compounds. |
baseline |
noise baseline, default 100 |
baselinesd |
standard deviation for noise, default 30 |
rf |
response factor of each compound, default 100 for all compounds |
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. |
one mzML file for simulated data and one csv file the simulated compounds with retention time, m/z and name
data(monams1)
simmzml(db=monams1, name = 'test')
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.