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. It annotates the resulting edges with community labels derived from the similarity network and retains only intra-community edges, so the edge file itself carries the community structure.
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,
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,
min_fragments = get_params(step =
"create_edges_spectra")\$ms\$thresholds\$ms2\$min_fragments,
resolution = 0.1,
n_iterations = 2L,
seed = NULL
)
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 |
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. |
min_fragments
|
integer Minimum number of fragment peaks a spectrum must have after cleaning to be retained |
resolution
|
numeric Resolution parameter for the Leiden/Louvain algorithm (higher values -> more, smaller communities). Default: 0.1. |
n_iterations
|
integer Number of iterations for the Leiden algorithm. Ignored for Louvain. Default: 2. |
seed
|
integer Random seed for reproducible clustering. If NULL, a random seed is used. Default: NULL.
|
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()