ChemSpider.annotation: ChemSpider.annotation

In jaspershen/MSannotator: xMSannotator: R package for network based annotation of metabolomics data.

Description

The ChemSpider annotation utility maps the input mz to known compounds in biological, chemical, and environmental databases. Users have the option to specify which data sources in ChemSpider should be used for annotaion. NOTE: Please obtain a security token from www.chemspider.com/Register.aspx before using this function. You will have to specify your role as a Service Subscriber.

Usage

ChemSpider.annotation(dataA, max.mz.diff = 10, queryadductlist = c("M+H"),
xMSannotator.outloc, numnodes = 1,
datasources = c("KEGG"), tokenstr = NA,
maxhits = 30,syssleep=5)

Arguments

dataA	Feature table from apLCMS or XCMS. The first column should be m/z.
max.mz.diff	Metlin matching m/z threshold in ppm. eg: 5
queryadductlist	List of adducts to be used for searching. eg: c("M+H","M+Na","M+K"), c("positive") for all positive ion adducts, or c("negative") for all negative ion adducts, or c("all") for all adducts as defined in Metlin.
xMSannotator.outloc	Output location where the HTML and text reports will be written. eg: "C:/experiment1/xMSanalyzeroutput/"
numnodes	Number of computing nodes to use. Default: 1
datasources	Provide a list of data sources to search against. The following data sources are supported: KEGG, Human Metabolome Database, LipidMAPS, MassBank, PubChem, BioCyc, SMPDB Small Molecule Pathway Database, EPA DSSTox, EPA Toxcast, Pesticide Common Names, ChEMBL, ChEBI, and NIST. The names of the data sources should be provided exactly as listed above. eg: c("KEGG", "PubChem", "EPA Toxcast", "Human Metabolome Database", "BioCyc")
tokenstr	Please register on ChemSpider website to obtain a security token. www.chemspider.com/Register.aspx Provide that security token here. Eg: "mysecuritycode"
maxhits	Maximum number of result hits to retrieve. Default: 30
syssleep	Wait time between queries. Default: 5

Details

This utility uses the ChemSpider web services to search for compounds based on the input mz, mass search threshold (+/- ppm), and adduct. The output is generated as an HTML report and a text file that includes pathway and compound annotations with links to several biological, chemical, and environmental databases. The function takes as input a data frame with a list of input m/z, a user-defined m/z threshold (ppm) to define the minimum and maximum mass range, list of adducts; eg: c(?M+H?, ?M+H-H2O?), the output folder location, list of data sources to be searched, and a security token string. ChemSpider_annotation_results.html

Value

A list is returned.

html.res	Annotation report in HTML format
text.res	Text delimited annotation report

Author(s)

Karan Uppal <[e-mail]>

jaspershen/MSannotator documentation built on May 18, 2019, 5:55 p.m.