Description Usage Arguments S3 METHODS References See Also Examples
Class slots:
an object of class setting
.
an object of class calibrator
.
1 2 3 4 5 |
dist.accel |
A numeric scalar denoting the distance from sample plate to first grid in millimeters. |
dist.drift |
A numeric scalar denoting the length of drift tube in meters. |
dist.focus |
A numeric scalar denoting the distance between charged grids in millimeters. |
error.rel |
A numeric vector denoting the relative calibration error for the calibrants. |
model |
An object of class |
time.delay |
A numeric scalar denoting the delay time before focus voltage is applied in nanoseconds. |
time.mean |
A numeric scalar denoting the mean time-of-flight of the calibrants. |
time.resol |
A numeric scalar denoting the time between detector records in seconds. |
vel0.mean |
A numeric scalar denoting the mean initial velocity in meters/second. |
vel0.std |
A numeric scalar denoting the standard deviation of initial velocity. |
volt.accel |
A numeric scalar denoting the voltage between charged grids in volts. |
volt.focus |
A numeric scalar denoting the voltage used in ion focusing phase in volts. |
Run a mass spectrometer.
Usage: run(simObj, proObj, isotope)
a spectrometer
object.
a proteins
object or a calibrants
object.
If proObj
is a calibrants
object, then a calibration run is performed
and a calibrated spectrometer
object is returned.
If proObj
is a proteins
object, then a real run is performed
and a spectrum
object is returned.
If the spectrometer
object has been calibrated,
the returned spectrum
will have values for both mz
slot and tof
slot.
Otherwise, the returned spectrum
will have values only for tof
slot.
a logical value indicating if isotope distribution should be simulated.
Coombes, K.R., Koomen, J.M., Baggerly, K.A., Morris, J.S., Kobayashi, R., “Understanding the characteristics of mass spectrometry data through the use of simulation," Cancer Informatics, 2005(1):41–52, 2005.
setting
, calibrator
, spectrum
, ion.focus.delay
.
1 2 3 4 5 6 7 8 9 10 11 | ## run a uncalibrated mass spectrometer
sam <- proteins(masses=c(1, 95, 190), counts=as.integer(c(500, 3000, 10000)))
sim <- spectrometer(vel0.mean=350, vel0.std=75, time.resol=4e-9)
x <- run(sim, sam)
plot(x)
## run a calibrated mass spectrometer
cal <- calibrants(masses=c(1000, 2000, 5000, 10000, 20000), counts=as.integer(rep(1000, 5)))
sim.cal <- run(sim, cal)
y <- run(sim.cal, sam)
plot(y)
|
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