SIM (version 1.42.0)

getPeak: 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, calcRI = 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.

calcRI

a function name to calculate RI 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

Value

• If multiple runs are provided, a list of list objects, one for each run. If a single run is provided, a list containing peaks information, i.e. the same as getEIC output.

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.

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)