chipPCR-package.Rd

\name{chipPCR-package}
\alias{chipPCR-package}
\alias{chipPCR}
\docType{package}
\title{
Toolkit of helper functions to pre-process amplification data
}
\description{
The \code{chipPCR} package is a toolkit of helper functions to pre-process 
amplification data. Amplification data can be obtained from classical PCR 
reactions or isothermal amplification reactions. The package contains 
functions to normalize amplification, a simple routine to detect the start of 
an amplification reaction and several smoothers for amplification data. The 
smoothers are based on LOWESS, moving average, cubic splines, Savitzky-Golay 
and others. In addition the first approximate approximate derivative maximum 
(FDM) and second approximate derivative maximum (SDM) can be calculated as 
quantification points from real-time amplification curves. \code{chipPCR} 
contains data sets of experimental nucleic acid amplification systems 
including the VideoScan HCU and a capillary convective PCR (ccPCR) system. 
The amplification data were generated by helicase dependent amplification 
(HDA) or polymerase chain reaction (PCR) under various temperature 
conditions. As detection system intercalating dyes (EvaGreen, SYBR Green) and 
hydrolysis probes (TaqMan) were used.
}
\details{
\tabular{ll}{
Package: \tab chipPCR\cr
Type: \tab Package\cr
Version: \tab 0.0.6\cr
Date: \tab 2014-04-15\cr
License: \tab GPL-3\cr
}
The function \code{\link[chipPCR]{bg.max}} can be used to remove missing 
values in amplification curve data. The function 
\code{\link[chipPCR]{amptester}} is used to test if an amplification is 
positive. \code{\link[chipPCR]{fixNA}} is used to impute missing values from 
a data column. \code{\link[chipPCR]{CPP}} can be used to normalize curve 
data, to remove background, to remove outliers and further steps. The package 
includes further functions to smooth the data by different functions 
including LOWESS, Moving Average, Friedman's SuperSmoother, Cubic Spline 
and Savitzky-Golay smoothing.
}
\author{
Stefan Roediger, Michal Burdukiewicz

Maintainer: Stefan Roediger <stefan.roediger@hs-lausitz.de>

}
\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}
}
\keyword{ chipPCR }
\seealso{
\link[qpcR]{qpcR.news}.
}
\examples{
# Example: A simple function to test for a background range.
# Data were taken form the chipPCR C17 data set.
data(C17)
plot(C17[, 2], C17[,  3], xlab = "time [min]", ylab = "Fluorescence", pch = 20)
res <- bg.max(C17[, 2], C17[, 3], bg.corr = 1.4, bg.start = 3, verbose = FALSE)
abline(v = c(res$bg.start, res$bg.stop), col = c(1,2))
abline(h = res$fluo, col = "blue")
}