Cy0 {qpcR}R Documentation

Cy0 alternative to crossing points/threshold cycles as in Guescini et al

Description

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.

Usage

Cy0(object, plot = FALSE, add = FALSE, ...)

Arguments

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.

Details

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).

Value

The Cy0 value.

Author(s)

Andrej-Nikolai Spiess

References

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.

Examples

## 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)) 

[Package qpcR version 1.2-4 Index]