expfit {qpcR}R Documentation

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.

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.

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.

Author(s)

Andrej-Nikolai Spiess

Examples

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

[Package qpcR version 1.0-6 Index]