dataList: Data list

In xdomingoal/erah-devel: Automated Spectral Deconvolution, Alignment, and Metabolite Identification in GC/MS-Based Untargeted Metabolomics

Data list

Description

The final eRah list of aligned and identified metabolites and their relative quantification for each sample in a given experiment

Usage

dataList(Experiment, id.database = mslib, by.area = TRUE)

## S4 method for signature 'MetaboSet'
dataList(Experiment, id.database = mslib, by.area = TRUE)

Arguments

Experiment	A 'MetaboSet' S4 object containing the experiment data. The experiment has to be previously deconvolved, aligned and identified.
id.database	The mass-spectra library to be compared with the empirical spectra. By default, the MassBank - Mass Bank of North America (MoNa) database are employed (mslib object).
by.area	if TRUE (default), eRah outputs quantification by the area of the deconvolved chromatographic peak of each compound. If FALSE, eRah outputs the intensity of the deconvolved chromatographic peak.

Details

Returns an identification and alignment table containing the list of aligned and identifed metabolites (names) and their relative quantification for each sample in a given experiment.

Value

alignList returns an S3 object:

AlignID	The unique Tag for found metabolite by eRah. Each metabolite found by eRah for a given experiment has an unique AlignID tag number.
tmean	The mean compound retention time.
FoundIn	The number of samples in which the compound has been detected (the number of samples where the compound area is non-zero).
Name.X	the name of the Xst/nd/rd... hit. idList return as many X (hits) as n.putative selected with identifyComp.
MatchFactor.X	The match factor/score of spectral similarity (spectral correlation).
DB.Id.X	The identification number of the library. Each metbolite in the reference library has a different DB.Id number.
CAS.X	the CAS number of each identified metabolite.
Quantification	As many columns as samples and as many rows as metabolites, where each column name has the name of each sample.

See Also

idList alignList

xdomingoal/erah-devel documentation built on Feb. 11, 2024, 11:11 a.m.