igDirect {CalciOMatic}R Documentation

Provide an Initial Guess For the Experiment-Specific Parameters of a Direct Fit

Description

The function igDirect provides an initial guess for the experiment-specific parameters of fluorescence transients obtained with a ratiometric dye (the background fluorescence log_S_B_340 and log_S_B_380, as well as the scaling coefficient log_phi)

Usage

igDirect(adu_B_340, adu_340, adu_B_380, adu_380,
         ig_ratio, t, tOn = 1, subset = 1:length(t),
         R_min = 0.136, R_max = 2.701, K_eff = 3.637, K_d = 0.583,
         B_T = 100, T_340 = 0.015, T_380 = 0.006, P = 400, P_B = 400)

Arguments

adu_B_340 the background fluorescence at 340 nm
adu_340 the fluorescence transient at 340 nm
adu_B_380 the background fluorescence at 380 nm
adu_380 the fluorescence transient at 380 nm
ig_ratio the initial guess list for the parameters of the Ca^2+ transient, returned by the igRatio function
t a vector of time values at which the fluorescence values were obtained (in s)
tOn the time of the fluorescence jump (in s)
subset a vector of time indices to consider (generally the whole fluorescence signals)
R_min the minimum fluorescence ratio between the measurements at 340 and 380 nm. This parameter is obtained from calibration experiments
R_max the maximum fluorescence ratio between the measurements at 340 and 380 nm. This parameter is obtained from calibration experiments
K_eff the effective dissociation constant of the dye in the cell (in muM). This parameter is obtained from calibration experiments
K_d the dissociation constant of the dye in the cell (in muM). This parameter is obtained from calibration experiments
B_T the total concentration of the dye in the cell (in muM)
T_340 the exposure time at 340 nm (in s)
T_380 the exposure time at 380 nm (in s)
P the number of pixels of the Region Of Interest (ROI)
P_B the number of pixels of the Background Region

Details

The intial guesses for log_S_B_340 and log_S_B_380 are obtained by averaging the adu_B_340 and adu_B_380 signals, divided by T_340*P_B and T_380*P_B respectively, and by taking their logarithm.

The initial guess for log_phi is obtained by applying a linear (zero-intercept) regression between the following signals, and by taking the logarithm of the slope:

c(adu_340/T_340/P - S_B_340, adu_380/T_380/P - S_B_380)

B_T / (K_d+Ca_ratio) * c(R_min*K_eff+R_max*Ca_ratio,K_eff+Ca_ratio)

In these formulas, Ca_ratio refers to the calcium concentration transient estimated with the initial guess of the parameters listed in the ig_ratio argument

Value

A named list of class "initial_guess", containing initial guesses (IG) for the logarithms of the three experiment-specific parameters: The background fluorescences at 340 and 380 nm (log_S_B_340 and log_S_B_380 respectively) and the amplitude coefficient log_phi

Author(s)

Sebastien Joucla sebastien.joucla@parisdescartes.fr

References

see the fluo documentation for details about the data generation model

See Also

igRatio, fluo

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

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

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

## 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

## Define Background and Transient fluorescence
## signals at 340 and 380 nm
adu_B_340 <- fluo(Ca=rep(0,nb_B),
                  R_min=R_min$value, R_max=R_max$value,
                  K_eff=K_eff$value, K_d=K_d$value,
                  B_T=0, phi=phi, S_B=S_B_340,
                  T_stim=T_340, P=P, P_B=P_B)

adu_340   <- fluo(Ca=Ca,
                  R_min=R_min$value, R_max=R_max$value,
                  K_eff=K_eff$value, K_d=K_d$value,
                  B_T=B_T, phi=phi, S_B=S_B_340,
                  T_stim=T_340, P=P, P_B=P_B)
  
adu_B_380 <- fluo(Ca=rep(0,nb_B),
                  R_min=1, R_max=1,
                  K_eff=K_eff$value, K_d=K_d$value,
                  B_T=0, phi=phi, S_B=S_B_380,
                  T_stim=T_380, P=P, P_B=P_B)

adu_380   <- fluo(Ca=Ca,
                  R_min=1, R_max=1,
                  K_eff=K_eff$value, K_d=K_d$value,
                  B_T=B_T, phi=phi, S_B=S_B_380,
                  T_stim=T_380, P=P, P_B=P_B)

## Add Poissonian noise to these signals
adu_B_340 <- rpois(length(adu_B_340), adu_B_340)
adu_340   <- rpois(length(adu_340), adu_340)
adu_B_380 <- rpois(length(adu_B_380), adu_B_380)
adu_380   <- rpois(length(adu_380), adu_380)

## Extract the noisy calcium transient
## (from the ratiometric transformation)
Ca_noisy <- caFromRatio(adu_B_340, adu_340,
                        adu_B_380, adu_380,
                        T_340, T_380,
                        P, P_B,
                        R_min, R_max, K_eff,
                        Plot = FALSE)

## Perform a ratiometric fit to determine
## the calcium dynamics parameters
ratio_fit <- ratioFitFromCa(Ca_noisy, t=Time, tOn, type="mono")

## List the fitted parameters and create
## the corresponding calcium transient
ig_mono <- as.list(ratio_fit$par)
names(ig_mono) <- c("log_Ca0","log_dCa","log_tau")
class(ig_mono) <- "initial_guess"

## Perform an Initial Guess for the Experiment-Specific Parameters
ig_direct <- igDirect(adu_B_340 = adu_B_340,
                      adu_340 = adu_340,
                      adu_B_380 = adu_B_380,
                      adu_380 = adu_380,
                      ig_ratio = ig_mono,
                      t = Time, tOn = tOn, subset = 1:length(Time),
                      R_min = R_min$value, R_max = R_max$value,
                      K_eff = K_eff$value, K_d = K_d$value,
                      B_T = 100, T_340 = T_340, T_380 = T_380, P = P, P_B = P_B)

## Compare the initial guess with the known values of the parameters
print(exp(as.vector(unlist(ig_direct))))
print(c(Ca0, dCa, tau, phi, S_B_340, S_B_380))

[Package CalciOMatic version 1.1-3 Index]