Hi Paul.
I have been trying to use your stitch method but I always get an error:
> temp = xcmsSet(file, lockMassFreq=TRUE)
20111213-001:
Error in if (length(by) && by == 0 && length(del) && del == 0) return(from) :
missing value where TRUE/FALSE needed
> traceback()
11: seq.default(from = start, to = length(object@scanindex), by = freq)
10: seq(from = start, to = length(object@scanindex), by = freq)
9: makeacqNum(object, freqLock, start)
8: makeacqNum(object, freqLock, start)
7: AutoLockMass(lcraw)
6: AutoLockMass(lcraw)
5: do.call(type, list(object, lockMass))
4: .local(object, lockMass, ...)
3: stitch(lcraw, AutoLockMass(lcraw))
2: stitch(lcraw, AutoLockMass(lcraw))
1: xcmsSet(file, lockMassFreq = TRUE)
Any ideas?
edit: In the paper you write that length of each gap is a parameter and defaults to 2. I cannot see a way to set that parameter. In my case there is only 1 lockmass scan per gap.