scorePairs: Calculate Pairwise Alignment Scores

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

Calculate Pairwise Alignment Scores

Description

Helper function for calcScores & evaluateParams. Calculates a pairwise similarity score between grouped features using differences in m/z, rt, and Q.

Usage

scorePairs(A, B, C, mzdiff, rtdiff, qdiff, rtrange, adductdiff)

Arguments

A	Numeric weight for penalizing m/z differences.
B	Numeric weight for penalizing differences between fitted & observed retention times.
C	Numeric weight for differences in Q (abundance quantiles).
mzdiff	Numeric differences between feature m/z values
rtdiff	Differences between model-projected retention time value & observed retention time
qdiff	Difference between feature quantile Q values
rtrange	Range of dataset Y retention times
adductdiff	Numeric divisors of computed score when non-empty adduct labels do not match

Details

The score between two grouped features x & y is calculated as:

S = -exp(-A |mzx - mzy| - B |rty - rtproj|/rtrange - C |Qx - Qy|)

where mzx & Qx correspond to the m/z and abundance quantile values of feature x; mzy, rty, and Qy correspond to the m/z, retention time, and quantile values of feature y; rtproj is the model-projected retention time of feature x onto the Y dataset chromatogram and rtrange is the retention time range of the Y dataset chromatogram. A, B, C are non-negative constant weight parameters for penalizing m/z, rt, and Q differences. Values between 0 (no confidence alignment) and 1 (high confidence alignment).

Value

Numeric similarity score between 0 & 1

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