This method resolves conflicting feature pair assignments
(labeled as "CONFLICT") to obtain 1-1 feature matches in the
combinedTable results report.
data frame containing the main
logical option to impose RT order for resolving subgroups
This is called from within
labelRows (with argument
resolveConflicts set to TRUE),
metabCombiner object inputs). The
method determines which combination of unique feature pairs has the highest
sum of scores ("resolveScore") within each subgroup. By default, these
combinations of feature pairs must have consistency in their retention time
order (rtOrder = TRUE). The combination of 1-1 feature pair alignments with
the highest resolveScore within the subgroups are annotated as "RESOLVED",
with the remaining unannotated rows labeled as "REMOVE" (or removed outright
by other package functions). Feature pairs belonging to multiple subgroup
(alt > 0) are labeled as REMOVE.
combinedTable fields, replacing "CONFLICT"
labels with "RESOLVED" or "REMOVE", depending on the computations performed.
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