scorePairs: Calculate Pairwise Alignment Scores

View source: R/calcScores.R

scorePairsR Documentation

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 June 5, 2024, 10:56 a.m.