desaturationAnalysis: Desaturation analysis of fatty acids.

In FAMetA: Fatty Acid Metabolic Analysis

Desaturation analysis of fatty acids.

Description

Desaturation analysis of fatty acids.

Usage

desaturationAnalysis(
  fadata,
  desaturationsdb = FAMetA::desaturationsdb,
  SEThr = 0.05
)

Arguments

fadata	fadata containing synthesis and elongation results.
desaturationsdb	desaturation reactions considered. It can be modified to change them or to add new reactions.
SEThr	minimum S or E value allowed to perform estimate desaturations.

Details

Once synthesis and elongation parameters have been estimated, these results can be used to calculate the FA fraction that comes from desaturation in unsaturated FA. For a given unsaturated FA (e.g. FA(18:1n9) we can conceptually consider a one-step elongation-desaturation reaction (in this example directly from FA(16:0) to FA(18:1n9) (E1') or a two-step elongation followed by desaturation process (in this example FA(16:0) is elongated to FA(18:0) (E1) and then desaturated to FA(18:1n9) (Des). Therefore, desaturation can be estimated based on the fraction of E1', which is E1 from FA(18:1)n9, and E1, which is E1 from FA(18:0). This same model can be used for all known desaturation steps (see FAMetA::desaturationsdb) as long as precursor and product FA isomers have been correctly and uniquely identified and stationary state has been reached.

Value

fadata list. Desaturation analysis results will be saved at the desaturation element of the fa list.

Author(s)

M Isabel Alcoriza-Balaguer <[e-mail]>

Examples

ssdata <- dataCorrection(ssexamplefadata, blankgroup="Blank")
ssdata <- synthesisAnalysis(ssdata, R2Thr = 0.95, maxiter = 1e3,
maxconvergence = 100, startpoints = 5)
ssdata <- elongationAnalysis(ssdata, R2Thr = 0.95, maxiter = 1e4,
maxconvergence=100, startpoints = 5, D2Thr = 0.1)
ssdata <- desaturationAnalysis(ssdata, SEThr = 0.05)


## Not run: 
fadata <- dataCorrection(examplefadata, blankgroup = "Blank")
fadata <- synthesisAnalysis(fadata, R2Thr = 0.95, maxiter = 1e3,
maxconvergence = 100, startpoints = 5)
fadata <- elongationAnalysis(fadata, R2Thr = 0.95, maxiter = 1e4,
maxconvergence=100, startpoints = 5, D2Thr = 0.1)
fadata <- desaturationAnalysis(fadata, SEThr = 0.05)

## End(Not run)

FAMetA documentation built on May 29, 2024, 8:16 a.m.