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 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.

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 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)

[Package qpcR version 1.1-8 Index]