batch_search {cmmr} | R Documentation |
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)
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 yl814@georgetown.edu
Georgetown University, USA
License: GPL (>= 3)
Examples
## Not run:
batch_search(c(670.4623, 1125.2555, 602.6180))
## End(Not run)
[Package cmmr version 0.1.2 Index]