getPeakScore {SIMAT} | R Documentation

## Calculate the similarity score for all peaks

### Description

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

### Usage

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

### Arguments

`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`.

### Details

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.

### Value

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

### Author(s)

Mo R. Nezami Ranjbar

### References

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

### See Also

`getScore`

### 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)

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

[Package SIMAT version 1.14.1 Index]