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xcmsSet problem
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
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