maxRatio {qpcR}R Documentation

The maxRatio method as in Shain et al

Description

The maximum ratio (MR) is determined along the interpolated curve of F(x)/F(x-1) and the corresponding cycle number at MR is taken. A measure of qPCR quality (FCN) is then calculated for the curve(s).

Usage

  maxRatio(ml, plot = TRUE, ...)

Arguments

ml an object of class 'modlist'.
plot Should diagnostic plots be displayed?
... other parameters to be passed to plot.

Details

In the original paper the authors smooth the datapoints and then apply a cubic spline on the ratio curve, in order to attain a resolution of 0.01 cycles. The function here calculates the ratio along a curve of the sigmoidal fit, which results in essentially the same.

Value

A list with the following components:

mr the maximum ratio.
fcn the cycle number at mr.
fcna a corrected fcn, as described in Shain et al.
names the names of the runs as taken from the original dataframe.

Author(s)

Andrej-Nikolai Spiess

References

A new method for robust quantitative and qualitative analysis of real-time PCR.
Shain & Clemens, Nucleic Acids Research, 2008, 36, e91.

Examples

ml <- modlist(reps, fct = l5()) 
maxRatio(ml)

[Package qpcR version 1.1-8 Index]