alignList: Alignment list

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

Alignment list

Description

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

Usage

alignList(object, by.area = TRUE)

## S4 method for signature 'MetaboSet'
alignList(object, by.area = TRUE)

Arguments

object	A 'MetaboSet' S4 object containing the experiment data. The experiment has to be previously deconvolved, aligned and (optionally) identified.
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 alignment table containing the list of aligned metabolites and their relative quantification for each sample in a given experiment.

Value

alignList returns a data frame 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.
Factor	the Factor tag name. Each metabolite has an unique 'Factor' name to enhance visual interpretation.
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).
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 dataList

erah documentation built on June 22, 2024, 11:01 a.m.