batch_eic {gcxgclab}

Finds batch of EICs

Description

batch_eic calculates the mass defect for each ion, then finds each listed EICs of interest.

Usage

batch_eic(data, MOIs, tolerance = 5e-04)

Arguments

data

a list object. Data extracted from a cdf file, ideally the output from extract_data().

MOIs

a vector object. A vector containing a list of all masses of interest to be investigated.

tolerance

a double object. The tolerance allowed for the MOI. Default is 0.0005.

Details

Extracted Ion Chromatogram (EIC) is a plot of intensity at a chosen m/z value, or range of values, as a function of retention time. This function uses find_eic() to find intensity values at the given mass-to-charge (m/z) values, MOIs, and in a range around MOI given a tolerance. Calculates the mass defect for each ion, then finds the specific EICs of interest. Returns a data frame of time values, mass values, intensity values,and mass defects.

Value

eic_list, list object, containing data.frame objects. Data frames of time values, mass values, intensity values, and mass defects for each MOI listed in the input csv or txt file.

Examples

file1 <- system.file("extdata","sample1.cdf",package="gcxgclab")
frame <- extract_data(file1,mod_t=.5)
mois <- c(92.1397, 93.07058)
eics <- batch_eic(frame, MOIs=mois ,tolerance = 0.005)
for (i in 1:length(eics)){
   print(plot_eic(eics[[i]], title=paste("EIC for MOI",mois[i])))
   print(plot_eic(eics[[i]], title=paste("EIC for MOI",mois[i]), dim=2))
}