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FAMetA (version 0.1.7)

Fatty Acid Metabolic Analysis

Description

Fatty acid metabolic analysis aimed to the estimation of FA import (I), de novo synthesis (S), fractional contribution of the 13C-tracers (D0, D1, D2), elongation (E) and desaturation (Des) based on mass isotopologue data.

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Version

Install

install.packages('FAMetA')

Monthly Downloads

270

Version

0.1.7

License

GPL (>= 2)

Maintainer

M Alcoriza-Balaguer

Last Published

July 29th, 2025

Functions in FAMetA (0.1.7)

Fit FA isotope distribution with non-linear regression using multiple starting points to find the best fit.

desaturationAnalysis

Desaturation analysis of fatty acids.

searchFAisotopes

Search FA isotopes

externalNormalization

External normalization using additional measures (i.e. protein levels).

generate starting points grid for synthesis analysis.

generate starting points grid for elongation analysis.

Get formula and neutral mass for annotated compounds

synthesisAnalysis

De novo synthesis analysis of fatty acids until 16 carbons.

Fatty Acids database.

Extract FA data from an annotated msbatch.

Plot results on a heatmap.

Plot observed and predicted isotope distributions from the results obtained.

Parameters for FA metabolic analysis.

read FA data from a csv file.

Add missing FA annotations

calculate FA isotope distribution for newly synthesized FAs using the quasi multinomial distribution.

blankSubstraction

substract blank samples.

Modify rt peak limits of annotated FAs

estimateSynthesis

estimate synthesis parameters.

runElongationAnalysis

run the elongation analysis.

getSummaryTable

Obtain a summary results table.

runSynthesisAnalysis

run synthesis analysis.

plotDistributions

Plot observed and predicted isotope distributions.

Example fadata list.

getResultsTable

Obtain the final results table from synthesis, elongation and desaturation analysis.

summarizeResults

Obtain result tables and heatmaps that help interpreting your results.

ssexamplefadata

Toy example fadata list.

Remove incorrect FA annotations

correctNatAb13C

correct data for natural abundance of 13C using accucor algorithm.

curateFAannotations

Modify FA annotations

Data correction for natural abundance of 13C and data normalization using internal standards followed by blank substraction.

data list for elongation analysis.

checkparameters

check S and E steps based on isotopologue distribution.

elongationAnalysis

Elongation analysis of fatty acids longer than 16 carbons.

Data normalization using internal stardards.

elongationqmult

calculate FA isotope distribution for elongated FAs using the quasi multinomial distribution.

acetate combinations for M+0, M+1 and M+2.

data list for synthesis analysis.

Fit FA isotope distribution with non-linear regression and calculate the sum of squared estimate of errors.

desaturationsdb

Desaturation reactions database.

mz match withing a vector of mz values

Search internal stardards.