feat.batch.annotation.KEGG: feat.batch.annotation.KEGG

In yufree/xMSanalyzer: xMSanalyzer: R package for data analysis, comparison, and annotation of metabolomics data.

Description

Batch annotation of features using KEGG REST for one or more adducts.

Usage

feat.batch.annotation.KEGG(dataA, max.mz.diff = 10, queryadductlist = c("M+H"), 
    xMSanalyzer.outloc, numnodes = 1, syssleep = 1)

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.
xMSanalyzer.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
syssleep	Wait time (seconds) in between queries. Default: 1

Details

This utility uses the readHTMLTable() function in the XML package in R and the KEGG REST interface to get the list of compounds and pathways IDs from KEGG. respectively. The output is generated as an HTML report and a text file that includes pathway and compound annotations with links to external databases such as KEGG Compound, KEGG Pathway, PubChem Substance, HMDB, ChEBI, CAS, and LipidMAPS. METLIN is no longer supported due to their updated terms of use. 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”), and the output folder location. A sample annotation report is available at the software homepage: SampleAnnotation.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]>

yufree/xMSanalyzer documentation built on May 4, 2019, 6:35 p.m.