Create spectral similarity network edges

Description

Calculates pairwise spectral similarity between all spectra to create a network edge list.

Usage

create_edges(
  frags,
  nspecs,
  precs,
  method,
  ms2_tolerance,
  ppm_tolerance,
  threshold,
  matched_peaks
)

Arguments

frags	List of aligned fragment spectra matrices
nspecs	Integer number of spectra
precs	Numeric vector of precursor m/z values
method	Similarity method ("entropy", "gnps", or "cosine")
ms2_tolerance	MS2 tolerance in Daltons
ppm_tolerance	PPM tolerance
threshold	Minimum similarity score threshold
matched_peaks	Minimum number of matched peaks required

Value

Data frame with columns: feature_id, target_id, score, matched_peaks. Returns empty data frame with NA values if no edges pass thresholds.

Examples

library("tima")

edges <- create_edges(
  frags = fragment_list,
  nspecs = length(fragment_list),
  precs = precursor_mz,
  method = "gnps",
  ms2_tolerance = 0.02,
  ppm_tolerance = 10,
  threshold = 0.7,
  matched_peaks = 6
)