msn2xcmsRaw {xcms} | R Documentation

## 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

### 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(s)

Steffen Neumann sneumann@ipb-halle.de

### 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")

[Package xcms version 3.2.0 Index]