mkFunction4DirectFit {CalciOMatic} | R Documentation |
The function mkFunction4DirectFit
returns a function
prediciting the exponential time course of fluorescence transients at
two wavelengths (including background fluorescence). The function, the
arguments of which depends on the value of type
, can be passed
to the nls
formula, for a direct fit
mkFunction4DirectFit(type = "mono", nb_B = 5, transients = 1, alphamethod = TRUE, SQRT = TRUE)
type |
a character string (either "mono" or "bi" ),
specifying which type of exponential decay should be considered |
nb_B |
the number of background measurements performed at each wavelength |
transients |
a vector of integers, specifying the numbers of the
transients to fit (determines the names of the calcium dynamics
parameters (log_Ca0_1 , log_Ca0_2 , ...)) |
alphamethod |
a logical value. Set to TRUE (respectively
FALSE ) to include alpha (respectively B_T ) in
the output function formals |
SQRT |
a logical value. Set to TRUE (the default value) to return the square root of the fluorescence signals |
A function, the arguments of which depend on the value of type
,
alphamethod
and transients
. The list below describes all
possible arguments:
t |
the times at which the fluorescence values are expected (in s) |
tOn |
the time of the fluorescence jump (in s) |
adu_B_340 |
the background fluorescence measurement(s) at 340 nm |
adu_340 |
the fluorescence transient(s) at 340 nm |
adu_B_380 |
the background fluorescence measurement(s) at 380 nm |
adu_380 |
the fluorescence transient(s) at 380 nm |
T_340 |
the exposure time at 340 nm |
T_380 |
the exposure time at 380 nm |
P |
the number of pixels of the ROI |
P_B |
the number of pixels of the background region |
log_Ca0_1 |
the logarithm of the Ca^2+ baseline of the first transient |
log_dCa_1 |
the logarithm of the Ca^2+ jump of the first transient |
log_tau_1 |
the logarithm of the Ca^2+ time constant of the first transient |
mu_1 |
the real number (between -Inf and +Inf )
defining the relative weight of the fast and slow time constants of
the Ca^2+ biexponential decay (if type is set to
"bi" ). The weight of the fast time constant is given by
exp(mu)/(1+exp(mu)) |
log_dtau_1 |
the logarithm of the dtau defining
the slow time constant of the Ca^2+ biexponential
decay (if type is set to TRUE"bi" ). This slow time
constant is given by tau_s=tau+dtau |
log_phi |
the logarithm of the experiment-specific amplitude coefficient |
log_S_B_340 |
the logarithm of the background fluorescence at 340 nm |
log_S_B_380 |
the logarithm of the background fluorescence at 380 nm |
log_R_min |
the logarithm of the minimum ratiometric measurement observable |
log_R_max |
the logarithm of the maximum ratiometric measurement observable |
log_K_eff |
the logarithm of the effective Fura dissociation constant in the cell (in muM) |
log_K_d |
the logarithm of the Fura dissociation constant (in muM) |
alpha |
the isocoefficient. Present only if alphamethod is
set to TRUE . In this case, B_T is replaced with
adu_340/(T_340*P) - adu_B_340/(T_340*P_B) +
alpha * (adu_380/(T_380*P) - adu_B_380/(T_380*P_B)) in the
fluorescence model |
B_T |
the total concentration of the dye in the cell. Present
only if alphamethod is set to FALSE |
Sebastien Joucla sebastien.joucla@parisdescartes.fr
## Parameters of the biexponential calcium transient tOn <- 1 Time <- seq(0,12,length.out=160) Ca0 <- 0.10 dCa <- 0.25 tau <- 1.5 mu <- 0 dtau <- 10 ## Calibrated parameters R_min <- 0.136 R_max <- 2.701 K_eff <- 3.637 K_d <- 0.583 ## Experiment-specific parameters B_T <- 100.0 T_340 <- 0.015 T_380 <- 0.006 P <- 200 P_B <- 200 phi <- 2 S_B_340 <- 30 S_B_380 <- 80 ## Define a function for fluorescence transients based on ## a monoexponential calcium concentration time course Fluo_bi_fct <- mkFunction4DirectFit(type = "bi", nb_B = 5, transients = 1, alphamethod = FALSE, SQRT = TRUE) ## Create the fluorescence transients Time <- matrix(Time, nrow=1, dimnames=list("1",NULL)) names(tOn) <- "1" Fluo_bi <- Fluo_bi_fct(t = Time, tOn = tOn, T_340 = T_340, T_380 = T_380, P = P, P_B = P_B, log_Ca0_1 = log(Ca0), log_dCa_1 = log(dCa), log_tau_1 = log(tau), mu_1 = mu, log_dtau_1 = log(dtau), log_phi = log(phi), log_S_B_340 = log(S_B_340), log_S_B_380 = log(S_B_380), log_R_min = log(R_min), log_R_max = log(R_max), log_K_eff = log(K_eff), log_K_d = log(K_d), B_T = B_T)