mkFunction4DirectFit {CalciOMatic}R Documentation

Function for Direct Fit

Description

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

Usage

mkFunction4DirectFit(type = "mono", nb_B = 5, transients = 1,
                     alphamethod = TRUE, SQRT = TRUE)

Arguments

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

Value

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

Author(s)

Sebastien Joucla sebastien.joucla@parisdescartes.fr

See Also

mkFluo4DirectFit, directFit

Examples

## 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)

[Package CalciOMatic version 1.1-3 Index]