batch_search: Encapsulation of CEU Mass Mediator batch search API

In lzyacht/cmmr: CEU Mass Mediator RESTful API

Description

batch_search returns the dataframe of all the database search results. using the following code to install the dependencies: install.packages(c("httr", "progress", "RJSONIO"))

Usage

  batch_search(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 = "[\"M+H\",\"M+Na\"]",
  tolerance = 10, tolerance_mode = "ppm", unique_mz)

Arguments

cmm_url	'http://ceumass.eps.uspceu.es/mediator/api/v3/batch' or your local API Endpoint
metabolites_type	"all-except-peptides", "only-lipids", "all-including-peptides"
databases	"all", "all-except-mine", "HMDB", "LipidMaps", "Metlin", "Kegg", "in-house", "mine"
masses_mode	"neutral", "mz"
ion_mode	"positive", "negative"
adducts	for positive mode [M+H, M+2H, M+Na, M+K,M+NH4, M+H-H2O]
tolerance	double (Range: [0..100])
tolerance_mode	"ppm", "mDa"
unique_mz	An array of unique m/zs

Value

dataframe for search results

Author(s)

Yaoxiang Li [e-mail]

Georgetown University, USA

License: GPL (>= 3)

Examples

## Not run: 
batch_search(c(670.4623, 1125.2555, 602.6180))

## End(Not run)

lzyacht/cmmr documentation built on July 1, 2021, 5:19 p.m.