Copy MSn data in an xcmsRaw to the MS slots

The MS2 and MSn data is stored in separate slots, and can not directly be used by e.g. findPeaks(). msn2xcmsRaw() will copy the MSn spectra into the "normal" xcmsRaw slots.

Usage

msn2xcmsRaw(xmsn)

Arguments

xmsn

an object of class xcmsRaw that contains spectra read with includeMSn=TRUE

Details

The default gap value is determined from the 90th percentile of the pair-wise differences between adjacent mass values.

Value

An xcmsRaw object

Author

Steffen Neumann sneumann@ipb-halle.de

See also

xcmsRaw,

Examples

 msnfile <- system.file("microtofq/MSMSpos20_6.mzML", package = "msdata")
 xrmsn <- xcmsRaw(msnfile, includeMSn=TRUE)
#> Create profile matrix with method 'bin' and step 1 ... 
#> OK
 xr <- msn2xcmsRaw(xrmsn)
 p <- findPeaks(xr, method="centWave")
#> Detecting mass traces at 25 ppm ... 
#> OK
#> Detecting chromatographic peaks in 10 regions of interest ...
#>  OK: 10 found.