main_labelling: Main function of the package

In RuggeroFerrazza/Lab_Project: A package for the analysis of MS isotopic patterns in labelling experiments

Description

It computes the estimated X abundances of each sample, returning an object of the class labelling.

Usage

main_labelling(peak_table, compound, charge = 1, labelling, mass_shift, RT,
  RT_shift, chrom_width, initial_abundance = NA)

Arguments

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)

Details

• 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

Value

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

Author(s)

Ruggero Ferrazza

Examples

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

RuggeroFerrazza/Lab_Project documentation built on May 9, 2019, 10:36 a.m.