qpcR (version 1.1-7)

maxRatio: 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.

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.

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.

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)