erah (version 2.0.1)

showRTRICurve: Show RT-RI curve

Description

This function uses RI of mslib database and RT of the identified compounds to discrimine proper compound identification.

Usage

showRTRICurve(
  Experiment,
  reference.list,
  nAnchors = 4,
  ri.thrs = "1R",
  id.database = mslib
)

Arguments

Experiment

S4 object with experiment Data, Metadata and Results. Results of experiment are used to extract RT and Compound DB Id.

reference.list

List with the compounds and their attributes (AlignId...)

nAnchors

The desired equivalent number of degrees of freedom for the smooth.spline function

ri.thrs

Retention Index treshold given by the user to discrimine bewteen identification results

id.database

Name of the preloaded database (mslib by default, the regular db used by erah)

Author

Xavier Domingo-Almenara. [e-mail]

Details

See eRah vignette for more details. To open the vignette, execute the following code in R: vignette("eRahManual", package="erah")

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

computeRIerror

Examples

if (FALSE) {
# The following set erah to determine which indetified compounds are in RI treshold
RTRICurve <- showRTRICurve(ex, list, nAnchors=4, ri.thrs='1R')
}