quantify.R script

This script is based on the same principle as checkRep.R (same input files), but aims to estimate the quantification parameters, such as the LOD.

Control variables

The job is defined by a few parameters.

taskTable  = 'files_quantification_2019July10.csv'
quantTable = 'targets_paper_quantification.csv'

fit_dim = 2
userTag = paste0('fit_dim_',fit_dim)

• taskTable: (string) file path to the list of experiments to be compared

• quantTable: (string) list of the compounds for which the comparisons should be done

• fit_dim: (integer) type of peak fit for which the comparisons should be done

• userTag: (string) tag to differentiate the outputs. In the present case, one wants to compare the repeatability for different peak fit approaches.

Outputs

Figures

A PDF file is generated, containing the quantification plots for all compounds.

The name of the file is a concatenation of the date, time, userTag, and ‘_quantif.pdf’

Tables

A ‘.csv’ table containing the quantification results.

The name of the file is a concatenation of the date, time, userTag, and ‘_quantif.csv’

Structure

Name	Int	Slo	Slo0	LOD

where

• Name is the name of the compound

• Int is the value of the intercept

• Slo is the value of the slope

• Slo0 is the value of the slope with null intercept

• LOD is the estimated limit of detection