transientConvexPart {CalciOMatic}R Documentation

Select the Convex or Concave Part of a Transient

Description

The functon transientConvexPart extracts the indices of a given transient where the signal is monotonically convex or concave, after a local peak (maximum or minimum) at the beginning of the transient

Usage

transientConvexPart(transient, t = 1, tOn = 1)

Arguments

transient the vector to work on
t a vector of time values at which transient has been obtained (in s)
tOn the time of the transient jump (in s)

Details

The function transientConvexPart is designed to work on transients of the following form: First, prior to tOn, a baseline; Then, at tOn, a sharp (positive or negative) jump, which leads to a global maximum or minimum; Finally, a monotonic return to baseline. Real Ca^2+ or fluorescence transients, on which this function is applied, are generally of this form. The function smoothes the input transient, finds the time (after the peak) at which the second derivative changes sign, and returns its index

Value

An integer, which is the index of the transient (after the peak) at which the second derivative changes sign, and returns its index

Author(s)

Sebastien Joucla sebastien.joucla@parisdescartes.fr

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 <- 0.136
R_max <- 2.701
K_eff <- 3.637
K_d   <- 0.583

## Experiment-specific parameters
nb_B <- 5
B_T <- 100.0
T_340 <- 0.015
T_380 <- 0.006
P <- 200
P_B <- 200
phi <- 20
S_B_340 <- 300
S_B_380 <- 800

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

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

## Get the fluorescence transients at 340 and 380 nm, respectively
t <- with(df_Mono,Time[!is.na(Time) & lambda==340])
adu_340 <- with(df_Mono,adu[!is.na(Time) & lambda==340])
adu_380 <- with(df_Mono,adu[!is.na(Time) & lambda==380])

## Calculate the indices of convex/concave starts at both wavelengths
idx_340 <- transientConvexPart(t = t, tOn = tOn, transient = adu_340)
idx_380 <- transientConvexPart(t = t, tOn = tOn, transient = adu_380)

## Plot both transients, with a specific color for the
## portions of interest
layout(matrix(c(1,2),ncol=1))

plot(t[c(1:idx_340)], adu_340[c(1:idx_340)], type="l",
     xlim = c(Time[1],Time[length(Time)]))
lines(t[c(idx_340:length(adu_340))],
      adu_340[c(idx_340:length(adu_340))], col="blue")

plot(t[c(1:idx_380)], adu_380[c(1:idx_380)], type="l",
     xlim = c(Time[1], Time[length(Time)]))
lines(t[c(idx_380:length(adu_380))],
      adu_380[c(idx_380:length(adu_380))], col="red")

[Package CalciOMatic version 1.1-3 Index]