sliwin {qpcR}R Documentation

Calculation of PCR efficiency by the window-of-linearity method

Description

A linear model is fit to a sliding window of the logarithmized raw fluorescence and the regression coefficient is calculated. At the point of maximum regression (log-linear range), the PCR efficiency is calculated.

Usage

  sliwin(object, wsize = 5, border = 7, plot = TRUE)

Arguments

object a 'drc' object.
wsize the size of the sliding window, default is 5.
border the -/+ border from the second derivative maximum cycle in which to do the fitting procedure.
plot if TRUE the result is plotted, if FALSE the result is diplayed on the console.

Details

To avoid fits with a high R-squared in the baseline region, the second derivative maximum is taken as a fixpoint. This value is consequently always near to the exponential region of the data and avoids the problem above. The efficiency is calculated by E = exp(slope), as the transformed raw data was based on the natural logarithm. The initial template fluorescence (F0) is thus calculated by F0 = exp(intercept).

Value

A list with the following components:

effmax the maximal PCR efficiency.
rmax the maximum R-squared.
init the initial template fluorescence F0.

Author(s)

Andrej-Nikolai Spiess

References

Assumption-free analysis of quantitative real-time polymerase chain reaction (PCR) data. Ramakers C et al., Neuroscience Letters, 2003, 339, 62-66.

Examples

m <- pcrfit(reps, 1, 2, l5())
sliwin(m)

[Package qpcR version 1.1-8 Index]