searchCMMR: Search CMMR

In MetaDBparse: Annotate Mass over Charge Values with Databases and Formula Prediction

Description

Queries Ceu Mass Mediator through their API

Usage

searchCMMR(
  cmm_url = "http://ceumass.eps.uspceu.es/mediator/api/v3/batch",
  metabolites_type = "all-except-peptides",
  databases = "[\"all-except-mine\"]",
  masses_mode = "mz",
  ion_mode = "positive",
  adducts = switch(ion_mode, positive =
    "[\"M+H\", \"M+2H\", \"M+Na\", \"M+K\", \"M+NH4\", \"M+H-H2O\"]",
    negative = "[\"M-H\", \"M+Cl\", \"M+FA-H\", \"M-H-H2O\"]"),
  tolerance = 10,
  tolerance_mode = "ppm",
  unique_mz
)

Arguments

cmm_url	API base url, Default: 'http://ceumass.eps.uspceu.es/mediator/api/v3/batch'
metabolites_type	Which type of metabolites to consider?, Default: 'all-except-peptides'
databases	Which databases to consider?, Default: '["all-except-mine"]'
masses_mode	Format of input compound, Default: 'mz'
ion_mode	Which ion mode was the compound found in?, Default: 'positive'
adducts	Adducts to be considered, Default: switch(ion_mode, positive = "[\"M+H\", \"M+2H\", \"M+Na\", \"M+K\", \"M+NH4\", \"M+H-H2O\"]", negative = "[\"M-H\", \"M+Cl\", \"M+FA-H\", \"M-H-H2O\"]")
tolerance	Error margin, units of 'tolerance_mode', Default: 10
tolerance_mode	Mode of error margin, Default: 'ppm'
unique_mz	M/z(s) to use in query

Value

Data table with match results

See Also

create_batch_body POST,content_type,content fromJSON progress_bar rbindlist

Examples

searchCMMR(unique_mz = "170.09240307", ion_mode = "positive")

MetaDBparse documentation built on May 3, 2021, 5:09 p.m.