create_advanced_batch_body: Create POST request Body for advanced batch search
In lzyacht/cmmr: CEU Mass Mediator RESTful API

View source: R/create-advanced-batch-body.R

create_advanced_batch_body

R Documentation

Create POST request Body for advanced batch search

Description

create_advanced_batch_body creates a list for the advanced batch search POST request.

Usage

create_advanced_batch_body(
  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

`chemical_alphabet`	A string for the chemical alphabet: "CHNOPS", "CHNOPSCL", "ALL".
`modifiers_type`	A string for the modifier type: "none", "NH3", "HCOO", etc.
`metabolites_type`	A string for metabolites type: "all-except-peptides", "only-lipids", etc.
`databases`	A vector of databases to search: e.g., list("HMDB").
`masses_mode`	A string specifying masses mode: "neutral" or "mz".
`ion_mode`	A string for the ionization mode: "positive", "negative", etc.
`adducts`	A vector of adducts to include in the search, e.g., list("M+H", "M+Na").
`deuterium`	Logical value: whether to consider deuterium substitutions (TRUE or FALSE).
`tolerance`	Numeric value specifying the tolerance.
`tolerance_mode`	A string for the tolerance mode: "ppm" or "mDa".
`masses`	Numeric vector of masses to search.
`all_masses`	Empty array for all masses (optional).
`retention_times`	Numeric vector of retention times.
`all_retention_times`	Empty array for retention times (optional).
`composite_spectra`	Empty array for composite spectra.
`all_composite_spectra`	A list for all composite spectra (optional)