msn2xcmsRaw: Copy MSn data in an xcmsRaw to the MS slots
In yclement/xcms: LC-MS and GC-MS Data Analysis

Description Usage Arguments Details Value Author(s) See Also Examples

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.

1	msn2xcmsRaw(xmsn)

xmsn

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

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

An xcmsRaw object

Steffen Neumann sneumann@ipb-halle.de

xcmsRaw,

 msnfile <- system.file("microtofq/MSMSpos20_6.mzML", package = "msdata")
 xrmsn <- xcmsRaw(msnfile, includeMSn=TRUE)
 xr <- msn2xcmsRaw(xrmsn)
 p <- findPeaks(xr, method="centWave")