getEIC {SIMAT} | R Documentation |
This function retrives the EIC of one peak in one run.
getEIC(Run = list(), compound = "Analyte", ms0 = numeric(), sp0 = numeric(), rt0 = numeric(), drt = 10/60, dsc = 10/2, ri0 = 0, weight = 2/3, deltaRI = 20, calibRI = NULL)
Run |
a list containing the information of one run obtained by |
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 |
calibRI |
a function to calculate retention index based on RI calibration information, can be obtained by |
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.
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 |
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 library retention time |
ri0 |
a numeric value of library retention index |
compound |
a character vector cintaining the name of the target. |
Mo R. Nezami Ranjbar
http://omics.georgetown.edu/SIMAT.html
# 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])