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 = 6L
)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 = 0.1,
matched_peaks = 1L,
assume_sanitized = FALSE
)
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 (default: 0.1). Pairs with similarity scores below this threshold are discarded to filter out random background noise and prevent memory overflow. Set to NULL to disable similarity thresholding and retain all pairwise comparisons.
|
matched_peaks
|
Minimum number of matched peaks required. Set to NULL to disable matched-peak filtering.
|
assume_sanitized
|
Boolean flag to assume if sanitize or not. FALSE |
Value
Data frame with columns: feature_id, target_id, score, matched_peaks. Returns empty data frame with NA values if no edges pass thresholds.
See Also
Other workflow: change_params_small(), create_components(), create_edges_spectra(), go_to_cache(), install(), install_tima(), run_app(), run_tima(), tima_full(), validate_inputs()