During peak picking and alignment, a valid peak group should appear in 50% of the data in at least one group in order to remain.
The underlying R code snippet:
#'@param minfrac, define the minimum fraction of samples necessary in at least one of the sample groups for
#'it to be a valid group
#'@param minsamp, define the minimum number of samples necessary in at least one of the sample groups for
#'it to be a valid group
# minfrac = 0.5, minsamp = 1,
….
# test for each grouped features (i.e. a single peak before alignment)
# default require at least half of samples per group
if (! any(gcount >= classnum*minfrac & gcount >= minsamp))
next # ignore
...