xcms (version 1.48.0)

msn2xcmsRaw: Copy MSn data in an xcmsRaw to the MS slots

Description

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

Value

An xcmsRaw object

Details

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

See Also

xcmsRaw,

Examples

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