View source: R/batch-search-advanced.R
advanced_batch_search | R Documentation |
advanced_batch_search
performs an advanced batch search on the CEU Mass Mediator API
and returns a dataframe of search results.
advanced_batch_search(
cmm_url = "https://ceumass.eps.uspceu.es/api/v3/advancedbatch",
chemical_alphabet = "ALL",
modifiers_type = "none",
metabolites_type = "all-except-peptides",
databases = "[\"HMDB\"]",
masses_mode = "mz",
ion_mode = "positive",
adducts = "[\"all\"]",
deuterium = FALSE,
tolerance = 7.5,
tolerance_mode = "ppm",
masses = NULL,
all_masses = "[]",
retention_times = NULL,
all_retention_times = "[]",
composite_spectra = NULL
)
cmm_url |
A character string specifying the CEU Mass Mediator API endpoint.
Default is |
chemical_alphabet |
A character string specifying the chemical alphabet to use.
Options are |
modifiers_type |
A character string specifying the modifier type.
Options are |
metabolites_type |
A character string specifying the metabolites type.
Options are |
databases |
A JSON-formatted character string specifying the databases to search.
Examples include |
masses_mode |
A character string specifying the masses mode. Options are |
ion_mode |
A character string specifying the ionization mode. Options are |
adducts |
A JSON-formatted character string specifying the adducts to include in the search.
Examples include |
deuterium |
A logical value indicating whether to consider deuterium substitutions. |
tolerance |
A numeric value specifying the mass tolerance (Range: |
tolerance_mode |
A character string specifying the tolerance mode. Options are |
masses |
A numeric vector of masses to search. |
all_masses |
A JSON-formatted character string representing an array of mass arrays. |
retention_times |
A numeric vector of retention times corresponding to the masses. |
all_retention_times |
A JSON-formatted character string representing an array of retention time arrays. |
composite_spectra |
A JSON-formatted character string representing composite spectra. |
A dataframe containing the search results from the CEU Mass Mediator API.
## Not run:
df <- advanced_batch_search(
cmm_url = "https://ceumass.eps.uspceu.es/api/v3/advancedbatch",
chemical_alphabet = "ALL",
modifiers_type = "none",
metabolites_type = "all-except-peptides",
databases = '["HMDB"]',
masses_mode = "mz",
ion_mode = "positive",
adducts = '["all"]',
deuterium = FALSE,
tolerance = 7.5,
tolerance_mode = "ppm",
masses = c(400.3432, 288.2174),
all_masses = "[]",
retention_times = c(18.842525, 4.021555),
all_retention_times = "[]",
composite_spectra = paste0(
'[ [ { "mz": 400.3, "intensity": 307034.9 },',
' { "mz": 311.2, "intensity": 400.1 } ] ]'
)
)
## End(Not run)
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