resolveRows: Resolve Conflicting Alignment Subgroups

In hhabra/Combiner: Method for Combining LC-MS Metabolomics Feature Measurements

Resolve Conflicting Alignment Subgroups

Description

This method resolves conflicting feature pair assignments (labeled as "CONFLICT") to obtain 1-1 feature matches in the combinedTable results report.

Usage

resolveRows(fields, rtOrder)

Arguments

fields	data frame containing the main
rtOrder	logical option to impose RT order for resolving subgroups

Details

This is called from within labelRows (with argument resolveConflicts set to TRUE), reduceTable, & metabCombiner (using 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.

Value

data.frame of combinedTable fields, replacing "CONFLICT" labels with "RESOLVED" or "REMOVE", depending on the computations performed.

hhabra/Combiner documentation built on Jan. 26, 2024, 10:30 p.m.