getEIC {SIMAT} | R Documentation

## Get the EIC of a peak

### Description

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

### Usage

    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)

### Arguments

`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.

### Details

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.

### Value

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.

### Author(s)

Mo R. Nezami Ranjbar

### References

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

### See Also

`getPeak`

### Examples

        # 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])

[Package SIMAT version 1.12.1 Index]