getEIC: Get the EIC of a peak

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

View source: R/getEIC.R

Description

This function retrives the EIC of one peak in one run.

Usage

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getEIC(Run = list(), compound = "Analyte", ms0 = numeric(), sp0 = numeric(),
                   rt0 = numeric(), drt = 10/60, dsc = 10/2, ri0 = 0, 
                   weight = 2/3, deltaRI = 20, calcRI = NULL)

Arguments

Run

a list containing the information of one run obtained by readCDf funciton.

compound

a character vector for the name of the target.

ms0

a numeric vector of mass of fragments of the target.

sp0

a numeric vector of intensities of fragments of the target.

rt0

a numeric value of the expected retention time of the target.

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

ri0

a numeric value of the retention index of the target from library, optional but recommended

deltaRI

a numeric value for the penalty on the retention index similarity score

weight

a numeric value in [0,1] interval to calculated a combined weighted similarity scores based on Apex and area under EIC curve

calcRI

a function name to calculate RI based on RI calibration information, can be obtained by getRI function, optional.

Details

This function accepts several parameters including the expected retention, the mass and intensity of several fragments, the retention index of the peak, the extracted data from a raw netCDF file in peak table format, a certain range for searching the retention time, i.e. the retention time window, average half peak width. The function uses a similarity score based on a combined measure from spectral matching and RI similarity, if RI is available, and finds the most appropriate peak in considering the target information.

Value

A list containing the peak information:

rtApex

a numeric value of retention time of the apex based on the quantifier fragment

intApex

a numeric value of the intensity of the quantifier fragment at its apex

RI

a numeric value of retention index related to the rtApex

area

area under EIC for all fragments of the related target

EIC

intensity of EIC profile of all fragments

RT

retention times of EIC profiles

ms

mass of fragments

sp

intensity of the fragments based on the reference spectrum

rt0

a numeric value of expected retention time

compound

a character vector cintaining the name of the target.

Author(s)

Mo R. Nezami Ranjbar

References

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

See Also

getPeak

Examples

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    # load an RData file including a single run data acquired by readCDF
    data("Run")
    
    # load targets information
    data(Targets)

    # get the corresponding peak of a target
    peakEIC <- getEIC(Run = Run, compound = Targets$compound[1], 
                    ms0 = Targets$ms[[1]], sp0 = Targets$sp[[1]], 
                    rt0 = Targets$rt[1], ri0 = Targets$ri[1])

Bioconductor-mirror/SIMAT documentation built on June 1, 2017, 1:15 a.m.