Cy0 {qpcR} | R Documentation |
An alternative to the classical crossing point/threshold cycle estimation as described in Guescini et al. A tangent is fit to the first derivative maximum (point of inflection) of the modeled curve and the intersect with the x-axis is calculated.
Cy0(object, plot = FALSE, add = FALSE, ...)
object |
a fitted object of class 'pcrfit'. |
plot |
if TRUE , displays a plot of Cy0. |
add |
if TRUE , a plot is added to any other existing plot, i.e. as from plot.pcrfit . |
... |
other parameters to be passed to plot.pcrfit or points . |
The function calculates the first derivative maximum (cpD1) of the curve and the slope and fluorescence at that point. Cy0 is then calculated by Cy0 = cpD1 - (Fluo/slope).
The Cy0 value.
Andrej-Nikolai Spiess
A new real-time PCR method to overcome significant quantitative inaccuracy due to slight amplification inhibition.
Guescini M et al, BMC Bioinformatics, 2008, 9: 326.
## single curve with plot m <- pcrfit(reps, 1, 2, l5) Cy0(m, plot = TRUE) ## add to 'efficiency' plot efficiency(m) Cy0(m, add = TRUE) ## compare s.d. of replicates between ## Cy0 and cpD2 method. cpD2 wins! ml <- modlist(reps, model = l4) cy0 <- sapply(ml, function(x) Cy0(x)) cpd2 <- sapply(ml, function(x) efficiency(x, plot = FALSE)$cpD2) tapply(cy0, gl(7, 4), function(x) sd(x)) tapply(cpd2, gl(7, 4), function(x) sd(x))