Description Usage Arguments Details Value Author(s) Examples
It computes the estimated X abundances of each sample,
returning an object of the class labelling
.
1 2 | main_labelling(peak_table, compound, charge = 1, labelling, mass_shift, RT,
RT_shift, chrom_width, initial_abundance = NA)
|
peak_table |
A data.frame containing the integrated signals for the samples |
compound |
The chemical formula of the compound of interest |
charge |
Natural number, denoting the charge state of the target adduct (1,2,3,...). If not provided, it is 1 by default |
labelling |
Character, either "H" or "C", specifying which is the labelling element |
mass_shift |
Maximum shift allowed in the mass range |
RT |
Expected retention time of the compund of interest |
RT_shift |
Maximum shift allowed in the retention time range |
chrom_width |
Chromatographic width of the peaks |
initial_abundance |
Initial estimate for the abundance of the heaviest X isotope (the label) |
peak_table: The first two columns of peak_table
represent the mass and the retention time of the peaks;
the other columns represent peak intensities for each sample.
The table can be obtained using the function table_xcms
compound: Character vector, where X has to represent the element with isotopic distribution to be fitted
initial_abundance: Numeric vector of the same length as the number of samples, with the initial estimate for the abundance of the heaviest X isotope (either ^2H or ^13C). If provided, number between 0 and 100. Otherwise, NA
An object of the class labelling
, which is a list containing the results from the fitting procedure:
compound |
Character vector specifying the chemical formula of the compound of interest, with X being the element with unknown isotopic distribution (to be fitted) |
Best_estimate |
Numeric vector representing the best estimated abundance of the heaviest X isotope (either ^2H or ^13C). Number between 0 and 100 |
std_error |
Numeric vector containing the standard errors of the estimates |
dev_percent |
The percentage deviations of the fitted theoretical patterns to the provided experimental patterns |
x_scale |
Vector containing the m/z signals of the isotopic patterns |
y_exp |
Matrix containing normalised experimental patterns, where for each sample the most intense signal is set to 100 |
y_theor |
Matrix of normalised fitted theoretical pattern (most intense signal set to 100 for each sample) |
residuals |
Matrix of residuals: each column is the difference between experimental and best fitted theoretical patterns |
warnings |
Character vector containing possible warnings coming from the fitting procedure |
Ruggero Ferrazza
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 | data(xcms_obj)
peak_table <- table_xcms(xcms_obj)
fitted_abundances <- main_labelling(peak_table,
compound="X40H77NO8P",
charge=1,
labelling="C",
mass_shift=0.05,
RT=285,
RT_shift=20,
chrom_width=7,
initial_abundance=NA)
summary(object=fitted_abundances)
plot(x=fitted_abundances, type="patterns", saveplots=FALSE)
plot(x=fitted_abundances, type="residuals", saveplots=FALSE)
plot(x=fitted_abundances, type="summary", saveplots=FALSE)
save_labelling(fitted_abundances)
grouped_estimates <- group_labelling(fitted_abundances,
groups=factor(c(rep("C12",4),
rep("C13",4))))
# Other possible lipid compounds include:
# [PC34:1 + H]+. compound="X42H83NO8P", RT=475, chrom_width=10
# [TAG47:3 + NH4]+(a minor species). compound="X50H94NO6",
# RT=891, chrom_width=7
|
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