fdyn: Retrieve flux dynamics from metabolic kinetics

Description

Retrieve flux dynamics from metabolic kinetics

Usage

fdyn(
  mf,
  stofull,
  nsp = 4L,
  nki = 5L,
  lieq = NULL,
  monotone = 0,
  dls = FALSE,
  atomlen = NULL,
  npi = 300L,
  wsd = FALSE,
  nmsf = character(0L),
  sderr = NULL,
  tol = 1e-10,
  regular_grid = TRUE
)

Value

List with following components:

mf:: specie data frame used for fitting
tp:: vector of time points for used measurements
tpp:: vector of time points for plot (fine time resolution)
sto:: stoichiometric matrix used for fitting
stofull:: stoichiometric matrix before a possible NA elimination
stoinv:: pseudo-inverse of sto
msp:: measured specie spline function
vsp:: estimated rates spline function
fsp:: estimated total flux (S*v) spline function
dsp:: first derivative of measured spline function
isp:: integrated specie spline function
asp:: atom balance over msp spline function
iasp:: atom balance over isp spline function
vsp:: flux spline function
dsp:: measured specie first derivative spline function
rsp:: residual dM/dt - S%*%v spline function
risp:: integral residual M - \u222bS%*%v dt spline function
sdrate:: matrix of SD values for flux B-spline coefficients, of size (ncoef x nrate)
chi2tab:: data-frame with chi2-test results
sf:: named scale factor vector
internal_knot_ref:: number of internal knots used for estimation of var_ref

Arguments

mf: Data-frame or matrix, specie kinetic measurements. Columns must be named with specie names and 'Time'.
stofull: Full stoichiometric matrix, stofull[i,j] means reaction 'j' produces specie 'i' with coeficient 'stofull[i,j]'. If stofull[i,j] < 0, the specie 'i' is consumed. Columns must be named with reaction names. Rows must be names with the species. "Full" in the name means that matrix includes even NA species.
nsp: Integer, polynomial order of B-spline to use for species (default 4)
nki: Integer, number of internal knots for B-splines (default 5)
lieq: List, equality constraints on species (default NULL, i.e. no equality constraint)
monotone: Numeric scalar or vector, 1=species are monotonically increasing; -1=monotonically decreasing; 0=no constraint. If vector, each value constraints (or not) a corresponding data column in mf ('Time' column is excluded from counting) (default 0, i.e. no monotonicity constraint)
dls: Logical scalar, if TRUE, indicates that differential least squares should be resolved instead of integral least squares. (default FALSE, i.e. ILS will be used)
atomlen: Numerical named vector, indicates what is label length of a given specie used a vector item name. If provided, results will contain lsp and ilsp fields which are a B-spline function representing atom balance over msp and isp splines. (default NULL, i.e. no atom balance will be provided)
npi: Integer scalar, indicates a number of plot intervals to produce smooth plots. (default 300)
wsd: Logical scalar, if TRUE, indicates that differential least squares should be resolved with residuals weighted by a factor of covariance matrix. (default FALSE, i.e. no weighting is used)
nmsf: Character vector, list of species for which scaling factor maust be estimated for --dls.
sderr: Numeric vector, use this SD of measured metabolites instead of automatically estimated. The name of each vector component is metabolite name, tha value is SD vale, e.g. c(GLC=0.1) (default NULL, i.e. SD are automatically estimated).
tol: Double scalar, tolerance for detecting singular matrices and solving linear systems
regular_grid: Logical scalar, use regular knot grid (default: TRUE)

Details

Each item in lieq corresponds to a specie and is a 2 column matrix (Time, Value). Each row of this matrix indicates what 'Value' must take corresponding specie at what 'Time'. Typically, it can be used to impose starting values at Time=0 for some species.
All specie fits are constraint to have values >= 0.