R/xMSannotator-package.R

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

#' xMSannotator
#' 
#' This package includes functions to perform metabolite annotation using HMDB,
#' KEGG, LipidMaps, T3DB, and selected data sources in ChemSpider.
#' 
#' The multilevelannotation() function uses a multi-criteria approach based on
#' data-driven modules, retention time, adducts, isotopes, mass defect, and
#' various chemical rules and ratio checks for assigning annotations into
#' different confidence levels: high (3), medium (2), low (1), and none (0).
#' The function is designed to work with KEGG, HMDB, T3DB, LipidMaps or a
#' custom database provided by the user. You can use status, origin, and
#' biofluid location arguments to select subset of metabolites in HMDB for
#' annotation.  The 'customIDs' argument can be used to only get confidence
#' levels for a subset of metabolites.
#' 
#' KEGG.annotation, T3DB. annotation, HMDB.annotation, LipidMaps.annotation,
#' and ChemSpider.annotation functions perform simple mz based annotaion based
#' on the user defined adducts and mass search threshold.
#' 
#' Additional utilites are provided for generating list of expected mz for
#' compounds based on KEGG pathway IDs, species IDs, and compound IDs. Users
#' can generate KEGG pathway map images and color code specific
#' metabolites/compounds.
#' 
#' \tabular{ll}{ Package: \tab xMSannotator\cr Type: \tab Package\cr Version:
#' \tab 1.3.2\cr Date: \tab 2017-06-29\cr License: \tab gpl2.0\cr LazyLoad:
#' \tab yes\cr }
#' 
#' @name xMSannotator_1.3.2-package
#' @aliases xMSannotator_1.3.2-package xMSannotator
#' @docType package
#' @author Karan Uppal Maintainer: <kuppal2@@emory.edu>
#' @references http://pubs.acs.org/doi/abs/10.1021/acs.analchem.6b01214
#' @keywords xMSannotator
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