runElongationAnalysis: run the elongation analysis.
In FAMetA: Fatty Acid Metabolic Analysis

runElongationAnalysis

R Documentation

run the elongation analysis.

Description

run the elongation analysis.

Usage

runElongationAnalysis(
  fa,
  M,
  D1,
  D2,
  P,
  S16,
  E1,
  E2,
  E3,
  E4,
  E5,
  R2Thr = 0.9,
  maxiter = 10000,
  maxconvergence = 100,
  startpoints = 5,
  D2Thr = D2Thr
)

Arguments

`fa`	data frame with isotope intensities for a FA. First two columns correspond to Compound and Label information.
`M`	total number of carbons for the FA.
`D1`	positive numeric between 0 and 1 specifying the contribution of acetate M+1. Estimated with synthesisAnalysis.
`D2`	positive numeric between 0 and 1 specifying the contribution of acetate M+2. Estimated with synthesisAnalysis.
`P`	overdispersion parameter. Estimated with synthesisAnalysis.
`S16`	fraction of newly synthesized C16 FA. If NA it is estimated. It is set to 0 for n3 and n6 FA series.
`E1`	fraction of elongated C18 FA from C16. If NA it is estimated. It is set to 0 for n3 and n6 FA series.
`E2`	fraction of elongated C20 FA from C18. If NA it is estimated.
`E3`	fraction of elongated C22 FA from C20. If NA it is estimated.
`E4`	fraction of elongated C24 FA from C22. If NA it is estimated.
`E5`	fraction of elongated C26 FA from C24. If NA it is estimated.
`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.