default.par <- par(no.readonly = TRUE)
# First Example
# Use mcaSmoother with different n to increase the temperature
# resolution of the melting curve artificially. Compare the
# influence of the n on the Tm and fluoTm values
data(MultiMelt)
Tm <- vector()
fluo <- vector()
for (i in seq(1,3.5,0.5)) {
res.smooth <- mcaSmoother(MultiMelt[, 1], MultiMelt[, 14], n = i)
res <- diffQ(res.smooth)
Tm <- c(Tm, res$Tm)
fluo <- c(fluo, res$fluoTm)
}
plot(fluo, Tm, ylim = c(76,76.2))
abline(h = mean(Tm))
text(fluo, seq(76.1,76.05,-0.02),
paste("n:", seq(3.5,1,-0.5), sep = " "), col = 2)
abline(h = c(mean(Tm) + sd(Tm), mean(Tm) - sd(Tm)), col = 2)
legend(-0.22, 76.2, c("mean Tm", "mean Tm +/- SD Tm"),
col = c(1,2), lwd = 2)
# Second Example
# Use mcaSmoother with different strengths of smoothing
# (f, 0.6 = strongest, 1 = weakest).
data(DMP)
plot(DMP[, 1], DMP[,6],
xlim = c(20,95), xlab = "Temperature",
ylab = "refMFI", pch = 19, col = 8)
f <- c(0.6, 0.8, 1.0)
for (i in c(1:3)) {
lines(mcaSmoother(DMP[, 1],
DMP[,6], df.fact = f[i]),
col = i, lwd = 2)
}
legend(20, 1.5, paste("f", f, sep = ": "),
cex = 1.2, col = 1:3, bty = "n",
lty = 1, lwd = 4)
# Third Example
# Plot the smoothed and trimmed melting curve
data(MultiMelt)
tmp <- mcaSmoother(MultiMelt[, 1], MultiMelt[, 14])
tmp.trimmed <- mcaSmoother(MultiMelt[, 1], MultiMelt[, 14],
Trange = c(49,85))
plot(tmp, pch = 19, xlab = "Temperature", ylab = "refMFI",
main = "MLC-2v, mcaSmoother using Trange")
points(tmp.trimmed, col = 2, type = "b", pch = 19)
legend(50, 1, c("smoothed values",
"trimmed smoothed values"),
pch = c(19,19), col = c(1,2))
# Fourth Example
# Use mcaSmoother with different n to increase the temperature
# resolution of the melting curve. Caution, this operation may
# affect your data negatively if the resolution is set to high.
# Higher resolutions will just give the impression of better
# data quality. res.st uses the default resolution (no
# alteration)
# res.high uses the double resolution.
data(MultiMelt)
res.st <- mcaSmoother(MultiMelt[, 1], MultiMelt[, 14])
res.high <- mcaSmoother(MultiMelt[, 1], MultiMelt[, 14], n = 2)
par(fig = c(0,1,0.5,1))
plot(res.st, xlab = "Temperature", ylab = "F",
main = "Effect of n parameter on the temperature
resolution")
points(res.high, col = 2, pch = 2)
legend(50, 1, c(paste("default resolution.", nrow(res.st),
"Temperature steps", sep = " "),
paste("double resolution.", nrow(res.high),
"Temperature steps", sep = " ")),
pch = c(1,2), col = c(1,2))
par(fig = c(0,0.5,0,0.5), new = TRUE)
diffQ(res.st, plot = TRUE)
text(65, 0.025, paste("default resolution.", nrow(res.st),
"Temperature steps", sep = " "))
par(fig = c(0.5,1,0,0.5), new = TRUE)
diffQ(res.high, plot = TRUE)
text(65, 0.025, paste("double resolution.", nrow(res.high),
"Temperature steps", sep = " "))
# Fifth example
# Different experiments may have different temperature
# resolutions and temperature ranges. The example uses a
# simulated melting curve with a temperature resolution of
# 0.5 and 1 degree Celsius and a temperature range of
# 35 to 95 degree Celsius.
#
# Coefficients of a 3 parameter sigmoid model. Note:
# The off-set, temperature range and temperature resolution
# differ between both simulations. However, the melting
# temperatures should be very
# similar finally.
b <- -0.5; e <- 77
# Simulate first melting curve with a temperature
# between 35 - 95 degree Celsius and 1 degree Celsius
# per step temperature resolution.
t1 <- seq(35, 95, 1)
f1 <- 0.3 + 4 / (1 + exp(b * (t1 - e)))
# Simulate second melting curve with a temperature
# between 41.5 - 92.1 degree Celsius and 0.5 degree Celsius
# per step temperature resolution.
t2 <- seq(41.5, 92.1, 0.5)
f2 <- 0.2 + 2 / (1 + exp(b * (t2 - e)))
# Plot both simulated melting curves
plot(t1, f1, pch = 15, ylab = "MFI",
main = "Simulated Melting Curves",
xlab = "Temperature", col = 1)
points(t2, f2, pch = 19, col = 2)
legend(50, 1,
c("35 - 95 degree Celsius, 1 degree Celsius per step",
"41.5 - 92.1 degree Celsius, 0.5 degree Celsius per step",
sep = " "), pch = c(15,19), col = c(1,2))
# Use mcaSmoother with n = 2 to increase the temperature
# resolution of the first simulated melting curve. The minmax
# parameter is used to make the peak heights compareable. The
# temperature range was limited between 45 to 90 degree Celsius for
# both simulations
t1f1 <- mcaSmoother(t1, f1, Trange= c(45, 90), minmax = TRUE, n = 2)
t2f2 <- mcaSmoother(t2, f2, Trange= c(45, 90), minmax = TRUE, n = 1)
# Perform a MCA on both altered simulations. As expected, the melting
# temperature are almost identical.
par(mfrow = c(2,1))
# Tm 77.00263, fluoTm -0.1245848
diffQ(t1f1, plot = TRUE)
text(60, -0.08,
"Raw data: 35 - 95 degree Celsius,\n 1 degree Celsius per step")
# Tm 77.00069, fluoTm -0.1245394
diffQ(t2f2, plot = TRUE)
text(60, -0.08, "Raw data: 41.5 - 92.1 degree Celsius,
\n 0.5 degree Celsius per step")
par(default.par)
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