cmmr (version 0.1.2)

batch_search: Encapsulation of CEU Mass Mediator batch search 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)

Value

dataframe for search results

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

Author

Yaoxiang Li

Georgetown University, USA

License: GPL (>= 3)

Examples

if (FALSE) {
batch_search(c(670.4623, 1125.2555, 602.6180))
}