getPeakScore: Calculate the similarity score for all peaks
In SIMAT: GC-SIM-MS data processing and alaysis tool

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

This function calculates and output the similarity scores based on spectral matching and RI similarity for multiple peaks.

1	getPeakScore(runPeaks = list(), deltaRI = 20, weight = 2/3, plot = FALSE)

`runPeaks`	a list of peaks of runs, e.g. generated by calling `getPeak`.
`deltaRI`	a numeric value for the penalty on the retention index similarity score
`weight`	a numeric value in [0,1] to calculated a combined weighted similarity scores based on Apex and area under EIC curve.
`plot`	a logical value to generate the histogram of the scores, default is `FALSE`.

By calling getScore(), this function calculates the similarity score for multiple peaks in multiple runs. This is performed by using spectral and retention index information together.

a matrix of scores with rows as compounds and columns as runs

Mo R. Nezami Ranjbar

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

getScore

    # 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)

    # get the scores for all analytes in all runs
    Scores <- getPeakScore(runPeaks = runPeaks)