Create edges spectra

Description

This function creates molecular network edges based on MS2 fragmentation spectra similarity. Compares all spectra against each other using spectral similarity metrics to identify related features.

Usage

create_edges_spectra(
  input = get_params(step = "create_edges_spectra")\$files\$spectral\$raw,
  output = get_params(step =
    "create_edges_spectra")\$files\$networks\$spectral\$edges\$raw\$spectral,
  name_source = get_params(step = "create_edges_spectra")\$names\$source,
  name_target = get_params(step = "create_edges_spectra")\$names\$target,
  method = get_params(step = "create_edges_spectra")\$similarities\$methods\$edges,
  threshold = get_params(step = "create_edges_spectra")\$similarities\$thresholds\$edges,
  matched_peaks = get_params(step =
    "create_edges_spectra")\$similarities\$thresholds\$matched_peaks,
  ppm = get_params(step = "create_edges_spectra")\$ms\$tolerances\$mass\$ppm\$ms2,
  dalton = get_params(step = "create_edges_spectra")\$ms\$tolerances\$mass\$dalton\$ms2,
  cutoff = get_params(step = "create_edges_spectra")\$ms\$thresholds\$ms2\$intensity,
  qutoff = deprecated()
)

Arguments

input character Path or list of paths to query MGF file(s) containing spectra
output character Path for output edges file
name_source character Name of source feature column
name_target character Name of target feature column
method character Similarity method to use
threshold numeric Minimum similarity threshold (0-1) to report edge
matched_peaks integer Minimum number of matched peaks required
ppm numeric Relative mass tolerance in ppm
dalton numeric Absolute mass tolerance in Daltons
cutoff numeric Intensity cutoff below which MS2 fragments are removed. Non-negative numeric or NULL for dynamic thresholding.
qutoff [Deprecated] Use cutoff instead.

Value

Character string path to the created spectral edges file

See Also

Other workflow: change_params_small(), create_components(), create_edges(), go_to_cache(), install(), install_tima(), run_app(), run_tima(), tima_full(), validate_inputs()

Examples

library("tima")

copy_backbone()
go_to_cache()
get_file(
  url = get_default_paths()$urls$examples$spectra_mini,
  export = get_params(step = "create_edges_spectra")$files$spectral$raw
)
create_edges_spectra()
unlink("data", recursive = TRUE)