erah (version 1.1.2)

computeRIerror: Retention Index Error Computation

Description

Computes the retention indexes (RI) errors given an internal or external calibration curve

Usage

computeRIerror(Experiment, id.database=mslib, reference.list, 
ri.error.type=c('relative','absolute'), plot.results=TRUE)

Value

Returns an 'Experiment' object. To visualize the output use: idList() function.

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).

reference.list

The list containing the reference data to create the calibration curve (Internal or external calibration). Please see the Vignette and Examples.

ri.error.type

Specify wether absolute or relative (default) RI error is to be computed.

plot.results

Shows the RI/RT graphic.

Author

Xavier Domingo-Almenara. [e-mail]

References

[1] Xavier Domingo-Almenara, et al., eRah: A Computational Tool Integrating Spectral Deconvolution and Alignment with Quantification and Identification of Metabolites in GC-MS-Based Metabolomics. Analytical Chemistry (2016). DOI: 10.1021/acs.analchem.6b02927

See Also

idList, dataList

Examples

if (FALSE) {

#Option A: (The RT and RI of an external calibration is provided)

ex <- computeRIerror(ex, mslib, reference.list=list(RT=c(4.4683, 7.4402, 8.8121, 11.5103), 
RI=c(1081.68, 1251.31, 1346.8, 1456.8)))
id.list <- idList(ex)

#Option B: (The AlignID of internally identified metabolites by
# eRah are provided, and used as a reference. )

ex <- computeRIerror(ex, mslib, reference.list=list(AlignID = c(45,67,92,120)))
id.list <- idList(ex) 

#Please, see Vignette for extended details.
}