getPeak: Get all peaks corresponding to targets in several runs
In SIMAT: GC-SIM-MS data processing and alaysis tool

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

This function retrives all the corresponding peaks of targets of interest in several runs.

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getPeak(Run = list(), file.name = character(), Targets = list(), 
            target.file.name = character(), drt = 10/60, dsc = 14/2, 
                weight = 2/3, deltaRI = 20, calibRI = NULL, rt.sort = FALSE)

`Run`	a list including a single run information, if provided, the next argument, i.e. file.name, is ignored.
`file.name`	a character vector of file names, i.e. the run file names generated by `readCDf`.
`Targets`	a list including the Targets information, e.g. acquired by `getTarget` function.
`target.file.name`	a character object, i.e. string, of the name of the file generated by `getTarget`.
`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
`weight`	a numeric value in [0,1] interval to calculated a combined weighted similarity scores based on Apex and area under EIC curve.
`deltaRI`	a numeric value for the penalty on the retention index similarity score.
`calibRI`	a function to calculate retention index based on RI calibration information, can be obtained by `getRI` function, optional.
`rt.sort`	a boolean value to sort the targets based on retention time before performing peak detection, optional

This function performs peak detection for a list of targets in several runs by calling getEIC. The list of targets should include the information on retention times, retention indexes, mass and intensity of the fragments. It can also include the name of the targets, i.e. compounds.

a list of list objects, one for each run. Each inner list represents a single run containing peaks information, i.e. the same as getEIC output.

Mo R. Nezami Ranjbar

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

getEIC

    # load an RData file including a single run data acquired by readCDF
    data("Run")
    
    # load targets information
    data(Targets)
    
    # get all the corresponding peaks of the target list
    runPeaks <- getPeak(Run = Run, Targets = Targets)