getPeak {SIMAT} | R Documentation

## Get all peaks corresponding to targets in several runs

### Description

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

### Usage

    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)

### Arguments

`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

### Details

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.

### Value

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.

### Author(s)

Mo R. Nezami Ranjbar

### References

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

### See Also

`getEIC`

### Examples

        # 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)

[Package SIMAT version 1.12.1 Index]