qpcR (version 1.0-6)

expfit: Calculation of PCR efficiency by fitting of an exponential model and minimization of residual variance

Description

An exponential model is fit to a sliding window of defined size along the qPCR data. In the window with minimal residual variance (or minimal AIC), the efficiency is calculated.

Usage

expfit(object, fitcyc = 5, plot = TRUE, crit = "resVar", start = 5, maxeff = 2, mineff = 1.5)

Arguments

object

a 'drc' object.

fitcyc

the size of the sliding window, default is 5.

plot

if TRUE the result is plotted, if FALSE the result is diplayed on the console.

crit

the criterium to be minimized. Either "resVar" or "AICc".

start

the cycle number to start from. Defaults to 5.

maxeff

the maximum allowed efficiency of the fit.

mineff

the minimum allowed efficiency of the fit. See Details.

Value

• A list with the following components:
• cyc.best
  the 'best' cycle with the minimized criterium.
• Eff.fit
  the PCR efficiency calculated from the exponential fit.
• Eff.curve
  the PCR efficiency for each cycle within the exponential phase. See Details.
• resVar
  the residual variance at the best cycle.
• AIC
  the AIC at the best cycle.
• RMSE
  the root-mean-squared error at the best cycle.
• init
  the initial template fluorescence, i.e. 'F0'.
• mod
  the exponential model from the best fit.

Details

The exponential growth function $f(x) = b * exp(k * x) + e$ is fit to the data. To avoid good fits in the plateau phase, the fitting procedure is stopped at cpD1 (first derivative maximum cycle). The efficiency is calculated a) from the exponential fit with $E = exp(d)$ (Eff.fit) and b) for each cycle within the exponential region from the raw fluorescence values by $E = \frac{F(n)}{F(n-1)}$ (Eff.curve). The inital template fluorescence (F0) is derived from parameter b. Avoiding good fits in the noisy ground phase can be tweaked by increasing the effmin parameter.

Examples

m <- multdrc(F1.1 ~ Cycles, data = reps, fct = l5())
expfit(m)
### using AIC as criterion
expfit(m, crit = "AIC")