files <- list.files("/home/zeleniy/workspace/mass/peaks/xcms", recursive=FALSE, full.names=TRUE)
xraw = xcmsRaw(
files,
profstep = 1,
profmethod = "intlin",
profparam = list(),
includeMSn=FALSE,
mslevel=NULL
)
peaks <- findPeaks.centWave(xraw, ppm=20, snthresh=5)
Execution:
zeleniy@zeleniy-HP-Pro-3400:~/workspace/mass/peaks$ Rscript xcms.r
Loading required package: methods
Detecting mass traces at 20 ppm ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
2778 m/z ROI's.
Detecting chromatographic peaks ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
1053 Peaks.
Set mslevel:
xraw = xcmsRaw(
files,
profstep = 1,
profmethod = "intlin",
profparam = list(),
includeMSn=FALSE,
mslevel=1
)
Execution:
zeleniy@zeleniy-HP-Pro-3400:~/workspace/mass/peaks$ Rscript xcms.r
Loading required package: methods
Error in function (classes, fdef, mtable) :
unable to find an inherited method for function "findPeaks.centWave", for signature "NULL"
Calls: findPeaks.centWave -> <Anonymous>
Execution halted
Why ?