advanced_batch_search: Advanced Batch Search using CEU Mass Mediator API

In lzyacht/cmmr: CEU Mass Mediator RESTful API

Advanced Batch Search using CEU Mass Mediator API

Description

advanced_batch_search performs an advanced batch search on the CEU Mass Mediator API and returns a dataframe of search results.

Usage

advanced_batch_search(
  cmm_url = "https://ceumass.eps.uspceu.es/mediator/api/v3/advancedbatch",
  chemical_alphabet = "all",
  modifiers_type = "none",
  metabolites_type = "all-except-peptides",
  databases = list("hmdb"),
  masses_mode = "mz",
  ion_mode = "positive",
  adducts = list("all"),
  deuterium = FALSE,
  tolerance = 10,
  tolerance_mode = "ppm",
  masses = c(399.3367, 421.3169, 315.2424, 337.2234, 280.2402),
  all_masses = list(),
  retention_times = c(18.8425, 18.8425, 8.1449, 8.1449, 28.2695, 4.0216),
  all_retention_times = list(),
  composite_spectra = list(),
  all_composite_spectra = list()
)

Arguments

cmm_url	A character string specifying the CEU Mass Mediator API endpoint.
chemical_alphabet	A character string specifying the chemical alphabet to use.
modifiers_type	A character string specifying the modifier type.
metabolites_type	A character string specifying the metabolites type.
databases	A list specifying the databases to search.
masses_mode	A character string specifying the masses mode.
ion_mode	A character string specifying the ionization mode.
adducts	A list specifying the adducts to include in the search.
deuterium	Logical value indicating whether to consider deuterium substitutions.
tolerance	A numeric value specifying the mass tolerance.
tolerance_mode	A character string specifying the tolerance mode.
masses	A numeric vector of masses to search.
all_masses	A list for arrays of masses (optional).
retention_times	A numeric vector of retention times corresponding to the masses.
all_retention_times	A list for retention times arrays (optional).
composite_spectra	A list for composite spectra (optional).
all_composite_spectra	A list for all composite spectra (optional)

Value

A dataframe containing the search results from the CEU Mass Mediator API.

Examples

df <- advanced_batch_search(
cmm_url = "https://ceumass.eps.uspceu.es/mediator/api/v3/advancedbatch",
chemical_alphabet = "all",
modifiers_type = "none",
metabolites_type = "all-except-peptides",
databases = list("hmdb"),
masses_mode = "mz",
ion_mode = "positive",
adducts = list("all"),
deuterium = FALSE,
tolerance = 10.0,
tolerance_mode = "ppm",
masses = c(399.3367, 421.31686, 315.2424, 337.2234, 280.2402),
all_masses = list(),
retention_times = c(18.842525, 18.842525, 8.144917, 8.144917, 28.269503, 4.021555),
all_retention_times = list(),
composite_spectra = list(),
all_composite_spectra = list()
)

head(df)

lzyacht/cmmr documentation built on Oct. 16, 2024, 4:06 p.m.