AmpSim.Rd

\name{AmpSim}
\alias{AmpSim}
%- Also NEED an '\alias' for EACH other topic documented here.
\title{
Amplification curve simulator
}
\description{
This function is a simple simulator of an amplification reaction based on a 
5-parameter Richards function.
}
\usage{
AmpSim(cyc = c(1:35), b.eff = -25, bl = 0.05, ampl = 1, Cq = 20, 
	noise = FALSE, nnl = 0.025, nnl.method = "constant")
}
%- maybe also 'usage' for other objects documented here.
\arguments{
  \item{cyc}{
    is a vector containing the cycle values.
}
  \item{b.eff}{
    can be used to adjust the amplification efficiency.
}
  \item{bl}{
	is used to define the base level (minimum) of the background range.
}
  \item{ampl}{
    defines the plateau (maximum) of the amplification reaction.
}
  \item{Cq}{
    defines approximately the quantification point (Cq) of the amplification 
    reaction.
}
  \item{noise}{
    adds some noise to the amplification reaction.
}
  \item{nnl}{
    level of noise during the amplification reaction.
}
  \item{nnl.method}{
    trend of noise level during the amplification reaction. "constant" uses same
    noise of amplification, "decreasing" leads to less noise at the end of the 
    amplification reaction, and "increasing" leads to more noise at the end of 
    the amplification reaction.
}
}
\details{
This function \code{AmpSim} is a simple simulator for amplification reaction. 
The function has several parameters which can be used to simulate the 
amplification curve. \code{b.eff} and \code{Cq} are most connected with 
another. Thus changing one of them will change both values. \code{Cq} can be 
used to define an approximate Cq value. The expression "approximate Cq value" 
is used here because the actual Cq value is dependent on the users preferred 
method (e.g., Cy0 method, Second Derivative Maximum (SDM) method, threshold 
method). The funtion can be used to see how an experimental system compares to 
a predicted model. Moreover it can be used to simulate data with noise, 
missing values (NA), signal-to-noise ratios, photo-bleaching and other 
influences on a PCR reaction.
}

\references{
A Highly Versatile Microscope Imaging Technology Platform for the Multiplex 
Real-Time Detection of Biomolecules and Autoimmune Antibodies. S. Roediger, 
P. Schierack, A. Boehm, J. Nitschke, I. Berger, U. Froemmel, C. Schmidt, M. 
Ruhland, I. Schimke, D. Roggenbuck, W. Lehmann and C. Schroeder. 
\emph{Advances in Biochemical Bioengineering/Biotechnology}. 133:33--74, 2013.
\url{http://www.ncbi.nlm.nih.gov/pubmed/22437246}

See also{\link[qpcR]{qpcR.news}}
}
\author{
Stefan Roediger, Michal Burdukiewicz
}

\examples{
# Example one
# Simulate a qPCR reaction with AmpSim for 40 cycles.
# Use an in-silico dilution of the template be adjusting 
# the Cq parameter. A change of 3.32 cycles corresponds 
# approximately to a 10-fold dilution.
par(mrfow = c(2,1))
plot(NA, NA, xlim = c(1,40), ylim = c(0.01,2), xlab = "Cycles", 
     ylab = "Fluorescence", main = "In-silco Dilution Experiment")
cycle.dilution <- seq(18, 35, 3.32)
for (i in 1:6) {
  lines(AmpSim(cyc = c(1:40), b.eff = -25, bl = 0.01, ampl = 2, 
	      Cq = cycle.dilution[i]), type = "b", col = i, pch = 20)
}

# Example two
# Simulate a qPCR reaction with AmpSim for 40 cycles and some noise.
plot(NA, NA, xlim = c(1,40), ylim = c(0.01,2.2), xlab = "Cycles", 
     ylab = "Fluorescence", 
     main = "In-silco Dilution Experiment with Some Noise")
cycle.dilution <- seq(18, 35, 3.32)
for (i in 1:6) {
  lines(AmpSim(cyc = c(1:40), b.eff = -25, bl = 0.01, ampl = 2, 
	      Cq = cycle.dilution[i], noise = TRUE, nnl = 0.05), 
	      type = "b", col = i, pch = 20)
}
par(mrfow = c(1,1))

# Example three
# Apply constant, increasing, decreasing nose to 
# amplification data.

par(mfrow = c(3,1))
method <- c("constant", "increase", "decrease")
for (j in 1:3){
    plot(NA, NA, xlim = c(1,40), ylim = c(0.02,2.2), xlab = "Cycles", 
	ylab = "Fluorescence", 
	main = paste("In-silco Dilution Experiment with noise method: ", 
					    method[j]))
    cycle.dilution <- seq(18, 35, 3.32)
    for (i in 1:6) {
      lines(AmpSim(cyc = c(1:40), b.eff = -25, bl = 0.02, ampl = 2, 
		   Cq = cycle.dilution[i], noise = TRUE, nnl = 0.08, 
		   nnl.method = method[j]), type = "b", col = i, pch = 20)
   }
}
par(mrfow = c(1,1))
}
% Add one or more standard keywords, see file 'KEYWORDS' in the
% R documentation directory.
\keyword{ simulation }
\keyword{ amplification }
\keyword{ Richards }
\keyword{ qPCR }