igRatio {CalciOMatic}R Documentation

Provide an Initial Guess For a Calcium Concentration Ratiometric Fit

Description

The function igRatio provides an initial guess for the parameters of an intracellular calcium concentration transient obtained after a ratiometric transformation. The transients considered here are either mono- or biexponential.

Usage

igRatio(Ca, t, tOn = 1, type = "mono")

Arguments

Ca a vector of Ca^2+ values (in muM)
t a vector of time values at which [Ca^2+] is computed (in s)
tOn the time of the [Ca^2+] jump (in s)
type a character string (either "mono" or "bi"), indicating which type of exponential decay to consider

Details

This function provides initial guesses for three or five parameters, depending on the type of exponential return to baseline. If type is set to "mono", three parameters are guessed:

If type is set to "bi", two more parameters (mu and log_dtau) are guessed. For that purpose, the slow time constant of the signal is first guessed: successive linear fits of the end part of the signal log-normalized signal (of increasing lengths, from T to Tend, with decreasing values of T) are performed, until the fitted time constant does not change anymore. Then, tau_s is set to T and its relative weight (from which mu arises) is deduced from the fit intercept. Considering the slope of the signal at the peak then leads to the fast time constant of the biexponential decay (tau), thus, to dtau.

Value

A named list of class "initial_guess", containing initial guesses (IG) for the three/five scalar following components of the mono- or bi- exponential calcium decay:

log_Ca0 IG for the logarithm of the baseline Ca^2+
log_dCa IG for the logarithm of the Ca^2+ jump
log_tau IG for the logarithm of the time constant of the monexponential decay (if type is set to "mono") or the fast time constant of the biexponential decay (if type is set to "bi")
mu IG for the real number (between -Inf and +Inf) defining the relative weight of the fast and slow time constants of the 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 IG for the logarithm of the dtau defining the slow time constant of the biexponential decay (if type is set to "bi"). This slow time constant is given by tau_s=tau+dtau

Author(s)

Sebastien Joucla sebastien.joucla@parisdescartes.fr

See Also

igDirect, caMonoBiExpFromIG

Examples

## Parameters of the monoexponential calcium transient
tOn <- 1
Time <- seq(0,12,length.out=160)
Ca0 <- 0.10
dCa <- 0.25
tau <- 1.5

## Calibration parameters
R_min <- list(value=0.136, mean=0.136, se=0.00363, USE_se=FALSE)
R_max <- list(value=2.701, mean=2.701, se=0.151,   USE_se=FALSE)
K_eff <- list(value=3.637, mean=3.637, se=0.729,   USE_se=FALSE)
K_d   <- list(value=0.583, mean=0.583, se=0.123,   USE_se=FALSE)

## Experiment-specific parameters
nb_B    <- 1
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

## Create a monoexponential calcium decay
Ca <- caMonoExp(t=Time,
                tOn=tOn,
                Ca0=Ca0,
                dCa=dCa,
                tau=tau)

## Simulate the corresponding ratiometric experiment
df <- ratioExpSimul(nb_B    = nb_B,
                    Ca      = Ca,
                    R_min   = R_min,
                    R_max   = R_max,
                    K_eff   = K_eff,
                    K_d     = K_d,
                    B_T     = B_T,
                    phi     = phi,
                    S_B_340 = S_B_340,
                    S_B_380 = S_B_380,
                    T_340   = T_340,
                    T_380   = T_380,
                    P       = P,
                    P_B     = P_B,
                    ntransients = 1,
                    G       = 1,
                    s_ro    = 0)

## Get the noisy calcium transient from the data frame
Ca_noisy <- caFromDf(df, numTransient=1, Plot=FALSE)

## Find an Initial Guess for the calcium transient parameters
ig_mono <- igRatio(Ca=Ca_noisy, t=Time, tOn=tOn, type="mono")

## Plot the simulated noisy calcium transient over the original
## calcium transient
plot(Time, Ca_noisy, type="l")
lines(Time, Ca, col="blue")

## Add the calcium transient corresponding to the initial guess
lines(Time, caMonoBiExpFromIG(t=Time, tOn=tOn, ig=ig_mono), lwd=2, col="red")

## Add the corresponding legend
legend("topright",c("Ideal","Noisy","Initial Guess"),
       col=c("blue","black","red"),lwd=c(1,1,2))

[Package CalciOMatic version 1.1-3 Index]