qpcR (version 1.1-7)

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

Description

An alternative to the classical crossing point/threshold cycles estimation as described in Guescini et al. A tangent is fit to the first derivative maximum (point of inflection) of the modeled curve and its intersection with the x-axis is calculated.

Usage

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

Arguments

object

a 'drc' object.

plot

if TRUE, displays a plot of Cy0.

add

if TRUE, plot can be added to any other existing plot, i.e. as from pcrplot.

...

other parameters to be passed to pcrplot or points.

Value

• The Cy0 value.

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 $Cy0 = cpD1 - (Fluo/slope)$.

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 Cy0's with cpD2's
ml <- modlist(reps, fct = l5())
sapply(ml, function(x) Cy0(x))
sapply(ml, function(x) efficiency(x, plot = FALSE)$cpD2)