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)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,
qutoff = get_params(step = "create_edges_spectra")\$ms\$thresholds\$ms2\$intensity
)
Arguments
input
|
Character string path or list of paths to query MGF file(s) containing spectra |
output
|
Character string path for output edges file |
name_source
|
Character string name of source feature column |
name_target
|
Character string name of target feature column |
method
|
Character string 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 |
qutoff
|
Numeric intensity cutoff below which MS2 fragments are removed |
Value
Character string path to the created spectral edges file