matchedFilter finds peaks in a EIC, with a max that is a parameter of the filter function. However, it looks like as soon as it hits one peak that fails the S/N threshold, it stops looking for more peaks in that EIC. This is in line 729 of xcmsRaw.R. Should it continue to look for other peaks, ignoring the current one? I've got a case where the highest one has low s/n, but there are other peaks in the EIC, at different RTs.
Thanks.
Not sure what you mean here. It should pick up all the relevant peaks above the noise threshold.
Can you give an example ?