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Create edges spectra

Source: R/create_edges_spectra.R
create_edges_spectra.Rd

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,
  threshold = get_params(step =
    "create_edges_spectra")$annotations$thresholds$ms2$similarity$edges,
  ppm = get_params(step = "create_edges_spectra")$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

threshold

Minimal similarity to report

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

if (FALSE) { # \dontrun{
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)
} # }