Create edges spectra

Description

This function create edges based on fragmentation spectra similarity

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,
  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,
  qutoff = get_params(step = "create_edges_spectra")\$ms\$thresholds\$ms2\$intensity
)

Arguments

input	Query file containing spectra. Currently an ‘.mgf’ file
output	Output file.
name_source	Name of the source features column
name_target	Name of the target features column
method	Similarity method
threshold	Minimal similarity to report
matched_peaks	Minimal number of matched peaks
ppm	Relative ppm tolerance to be used
dalton	Absolute Dalton tolerance to be used
qutoff	Intensity under which ms2 fragments will be removed.

Value

The path to the created spectral edges

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)