getEIC: Get the EIC of a peak
In SIMAT: GC-SIM-MS data processing and alaysis tool

Description Usage Arguments Details Value Author(s) References See Also Examples

This function retrives the EIC of one peak in one run.

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getEIC(Run = list(), compound = "Analyte", ms0 = numeric(), sp0 = numeric(),
                   rt0 = numeric(), drt = 10/60, dsc = 10/2, ri0 = 0, 
                   weight = 2/3, deltaRI = 20, calibRI = NULL)

`Run`	a list containing the information of one run obtained by `readCDf` funciton.
`compound`	a character vector for the name of the target.
`ms0`	a numeric vector of mass of fragments of the target.
`sp0`	a numeric vector of intensities of fragments of the target.
`rt0`	a numeric value of the expected retention time of the target.
`drt`	a numeric value of the retention time window width in seconds, optional but recommended
`dsc`	a numeric value of average half peak width based on the TICs, optional but recommended
`ri0`	a numeric value of the retention index of the target from library, optional but recommended
`deltaRI`	a numeric value for the penalty on the retention index similarity score
`weight`	a numeric value in [0,1] interval to calculated a combined weighted similarity scores based on Apex and area under EIC curve
`calibRI`	a function to calculate retention index based on RI calibration information, can be obtained by `getRI` function, optional. It is also used to estimate the retention time related to a retention index.

This function accepts several parameters including the expected retention, the mass and intensity of several fragments, the retention index of the peak, the extracted data from a raw netCDF file in peak table format, a certain range for searching the retention time, i.e. the retention time window, average half peak width. The function uses a similarity score based on a combined measure from spectral matching and RI similarity, if RI is available, and finds the most appropriate peak in considering the target information.

A list containing the peak information:

`rtApex`	a numeric value of retention time of the apex based on the quantifier fragment
`intApex`	a numeric value of the intensity of the quantifier fragment at its apex
`RI`	a numeric value of retention index related to the `rtApex`
`area`	area under EIC for all fragments of the related target
`EIC`	intensity of EIC profile of all fragments
`RT`	retention times of EIC profiles
`ms`	mass of fragments
`sp`	intensity of the fragments based on the reference spectrum
`rt0`	a numeric value of library retention time
`ri0`	a numeric value of library retention index
`compound`	a character vector cintaining the name of the target.

Mo R. Nezami Ranjbar

http://omics.georgetown.edu/SIMAT.html

getPeak

    # load an RData file including a single run data acquired by readCDF
    data("Run")
    
    # load targets information
    data(Targets)

    # get the corresponding peak of a target
    peakEIC <- getEIC(Run = Run, compound = Targets$compound[1], 
                    ms0 = Targets$ms[[1]], sp0 = Targets$sp[[1]], 
                    rt0 = Targets$rt[1], ri0 = Targets$ri[1])