xcmsSet problem

[bernt-matthias]

When using xcmsSet with

Scan range option | hide |  
Extraction method for peaks detection | centWave |  
Max tolerated ppm m/z deviation in consecutive scans in ppm | 25 |  
Min,Max peak width in seconds | 10,35 |  
Advanced options | show |  
Signal/Noise threshold | 10 |  
Minimum difference in m/z for peaks with overlapping retention times | 0.05 |  
peak limits method | peak limits based on smoothed 2nd derivative (less precise) |  
Prefilter step for the first phase | 3,100 |  
Noise filter | 0

on

Sihumi_IPP_A1.mzML.gz

I get the following error:

Error in seq.default(object@scanindex[scan] + 1, min(object@scanindex[scan +  : 
  'from' must be of length 1
Calls: do.call ... .local -> getScan -> getScan -> .local -> seq -> seq.default
In addition: Warning message:
In `[<-`(`*tmp*`, "object", value = <S4 object of class "xcmsRaw">) :
  implicit list embedding of S4 objects is deprecated
Execution halted

I guess there is something wrong with the data, but I do not understand xcms well enough.

I tried to debug a bit but got confused

Apparently in xcms.r the last call is xset = do.call(thefunction, listArguments) which calls xcmsSet with the parameters:

[[1]]
[1] "."

$nSlaves
[1] 1
$method
[1] "centWave"
$ppm
[1] 25
$peakwidth
[1] 10 35
$mzdiff
[1] 0.05
$snthresh
[1] 10
$integrate
[1] 1
$noise
[1] 0
$prefilter
[1]   3 100

But none of these parameters is documented in: https://bioconductor.org/packages/release/bioc/manuals/xcms/man/xcms.pdf