scoreIsotopes: Calculate Isotopic Pattern Similarity Scores

In enviGCMS: GC/LC-MS Data Analysis for Environmental Science

Calculate Isotopic Pattern Similarity Scores

Description

Computes modern spectral similarity metrics including Cosine similarity, intensity-weighted dot product, and log-likelihood between observed mass spectral peaks and theoretical isotopic distributions.

Usage

scoreIsotopes(
  obs_mz,
  obs_int,
  theo_mz,
  theo_int,
  tolerance = 0.005,
  ppm = FALSE
)

Arguments

obs_mz	Numeric vector of observed m/z values.
obs_int	Numeric vector of observed intensities.
theo_mz	Numeric vector of theoretical isotopic m/z values.
theo_int	Numeric vector of theoretical isotopic abundances.
tolerance	Numeric mass tolerance for peak alignment (default: 0.005).
ppm	Logical indicating whether tolerance is in ppm (default: FALSE).

Value

A list containing:

cosine	Cosine similarity (unweighted dot product of normalized spectra).
weighted_cosine	Mass- and intensity-weighted dot product (MassBank/NIST style).
log_likelihood	Multinomial log-likelihood of observed peak distribution.
matched_peaks	Integer count of successfully matched peaks.

Examples

obs_m <- c(180.0634, 181.0668)
obs_i <- c(100, 6.5)
theo_m <- c(180.0634, 181.0668)
theo_i <- c(1.0, 0.066)
scoreIsotopes(obs_m, obs_i, theo_m, theo_i)

enviGCMS documentation built on Oct. 10, 2026, 5:06 p.m.