Re: sequential addition of files to an xcms object
Reply #1 –
As far as I'm aware this isn't possible. The retention time correction using the obiwarp method for example has to be reassessed with a new centre sample.
See the help file
?retcor.obiwarp
#center
#the index of the sample all others will be aligned to. If center==NULL, the sample with the most peaks is chosen as default
So the retention time deviation for each file has to be re-calculated.
Additionally for grouping the minfrac and minsamp arguments will be affected by additional samples in each group as you concatenate.
?group.density
#minfrac
#minimum fraction of samples necessary in at least one of the sample groups for it to be a valid group
#minsamp
#minimum number of samples necessary in at least one of the sample groups for it to be a valid group
It shouldn't be (computationally speaking) too much of a big deal to re-do the retention time correction and grouping each time you peak-pick an additional file(s). The most time-consuming part is definitely the xcmsSet function.