objective: Weight Parameter Objective Function

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

Weight Parameter Objective Function

Description

This function evaluates the A, B, C weight parameters in terms of score separability of matching versus mismatching compound alignments. Higher objective function value imply a superior weight parameter selection.

Usage

objective(
  cTable,
  idtable,
  A,
  B,
  C,
  minScore,
  mzdiff,
  rtdiff,
  qdiff,
  rtrange,
  adductdiff,
  penalty,
  matches,
  mismatches
)

Arguments

cTable	data frame. Abridged metabCombiner report table.
idtable	data frame containing all evaluated identities
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).
minScore	numeric. Minimum score to count towards objective value.
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
penalty	positive numeric penalty wherever S(i,j) > S(i,i), i =/= j
matches	integer row indices of identity matches
mismatches	list of integer identity row mismatches for each identity

Details

First, the similarity scores between all grouped features are calculated as described in scorePairs

Then, the objective value for a similarity S is evaluated as:

OBJ(S) = \sum h(S(i,i)) - h(S(i, j)) - p(S(i,i) > S(i,j))

-S(i,i) represents the similarity between correct identity alignments
-S(i,j), represents the maximum similarity of i to grouped feature j, i =/= j (the highest-scoring misalignment)
-h(x) = x if x > minScore, 0 otherwise
-p(COND) = 0 if the condition is true, and a penalty value otherwise

This is summed over all labeled compound identities (e.g. idx = idy) shared between input datasets.

Value

A numeric value quantifying total separability of compound match similarity scores from mismatch scores, given A,B,C values

hhabra/metabCombiner documentation built on Jan. 26, 2024, 12:23 p.m.