FAMetA (version 0.1.7)

elongationAnalysis: Elongation analysis of fatty acids longer than 16 carbons.

Description

Elongation analysis of fatty acids longer than 16 carbons.

Usage

elongationAnalysis(
  fadata,
  R2Thr = 0.98,
  maxiter = 10000,
  maxconvergence = 100,
  startpoints = 5,
  D2Thr = 0.1,
  parameters = FAMetA::parameters,
  verbose = TRUE
)

Value

fadata list. Elongation analysis results will be saved at the elongation element of the fa list.

Arguments

fadata

fadata containing synthesis results.

R2Thr

positive numeric between 0 and 1 specifying the minimum R2 allowed for fits.

maxiter

parameter passed to nls.control. Positive integer specifying the maximum number of iterations allowed.

maxconvergence

positive integer specifying the maximum number of successes before choosing the winning model.

startpoints

positive integer specifying the number of starting points for each parameter to be estimated.

D2Thr

minimum D2 value allowed to perform the elongation analysis.

parameters

parameters to be estimated for each fatty acid. It can be modified to change them or to add new fatty acids (adding new rows).

verbose

print information messages.

Author

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

Details

Main route of de novo synthesis plus elongation starts at 16 carbons and then adds blocks of 2 carbons. Therefore, isotopologue distributions for FA longer than 16 carbons will be modeled taking into account de novo synthesis until FA(16:0), followed by single and independent elongation steps (E1, E2 …, En). Parameters D0, D1 and D2 are imported from FA(16:0) or FA(14:0) and thus, the only relevant parameters to be estimated in the elongation analysis are Ei and I. For n6 and n3 series, elongation is expected from FA(18:2)n6 and FA(18:3)n3 so that synthesis (S16:0) and first elongation step (E1) are set to 0.

Examples

# \donttest{
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)
# }

if (FALSE) {
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)
}