SIM (version 1.42.0)

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

Arguments

runPeaks

a list of peaks of one run, e.g. generated by calling getPeak.

dsPeaks

a list of lists, each, containing peaks of one run, e.g. generated by calling getPeak where ds stands for a data set.

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.

Value

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

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.

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)