evAnnotate: Annotation by Everest

In xdomingoal/everest: Annotation and Identification in LC/MS-Based Untargeted Metabolomics

Description

Annotation of features detected by XCMS or a list of features detected by other software

Usage

evAnnotate(xcmsSet=NULL, data.table=NULL, 
ion.mode=c('pos','neg'), min.correlation=0.7, 
max.time.dist=1, ppm.error=20, max.mz.error=0.05,
annRules=everestRules, db.object=hmdb, fluidType=NULL,
topAdductsN=4, import.profiles=FALSE,
alternative.data.path=NULL)

Arguments

xcmsSet	A 'xcmsSet' S4 object containing the experiment data previously created by XCMS.
data.table	A data table containing the list of features (see Details)
ion.mode	Character. Wether positive 'pos' or negative 'neg' type of study.
min.correlation	The mininmum abundance correlation among samples for which pairs of features are considered to be from the same compound.
max.time.dist	The maximum retention time distance (in seconds) for which pairs of features might be considered to be from the same compound.
ppm.error	The m/z error un parts per milion (ppm) in which annotations are performed
max.mz.error	Despite the ppm.error, the maximum absolute error (in Da) for adduct annotation.
annRules	Annotation Rules (see Details)
db.object	Database used for result-filtering. Use NULL if no filtering is to be applied.
fluidType	If a database is used for filtering (db.object), select type of fluid.
topAdductsN	Integer, cut-off number of prioritized adduct that remain as top-candidate adducts.
import.profiles	If TRUE, EIC are imported from the XCMS object (currently not implemented).
alternative.data.path	Alternative path when the data path is not the same as in the XCMS object (currently not implemented).

Details

See eveRest vignette for more details. To open the vignette, execute the following code in R: vignette("eveRestManual", package="everest")

Value

The function returns an updated S4 'MetaboSet' class, where the LC-MS peaks have been annotated.

Author(s)

Xavier Domingo-Almenara. [e-mail]

References

[1] Xavier Domingo-Almenara, et al., eveRest: A Computational Tool for Metabolite Annotation in LC/MS-Based Metabolomics. Anal. Chem (2018) Submitted.

See Also

showAn, annoTable

Examples

## 1a. Annotate compounds (from XCMS):

	#ex <- evAnnotate(xcmsSet=xset3, data.table=NULL, 
	#ion.mode='pos', min.correlation=0.6, max.time.dist=1, 
	#ppm.error=20, max.mz.error=0.05, annRules=annRules, 
	#import.profiles=FALSE, alternative.data.path=NULL)

## 1b. Annotate compounds (from Data Table):

	#ex <- evAnnotate(data.table=sample.tab, ion.mode='pos', 
	#min.correlation=0.6, max.time.dist=1, ppm.error=20, 
	#max.mz.error=0.05, annRules=annRules)

	#showAn(ex, 'M112T102') 
	#anTab <- annoTable(ex) 

## 2. Identify compounds:

	#ex <- evIdentify(ex, db=hmdb, ppm.error=5)

	#showId(ex, 'M112T102') 	
	#idTab <- idenTable(ex) 

xdomingoal/everest documentation built on May 17, 2019, 11:08 a.m.