PCRedux (version 1.2-0)

hookregNL: hookregNL - A function to calculate the slope of amplification curves in the tail region

Description

hookregNL is a function to calculate the slope and intercept of an amplification curve from a quantitative PCR experiment. The idea is that a strong negative slope at the end of an amplification curve is indicative for a hook effect (see Barratt and Mackay 2002). In contrast to hookreg fits this function a sex-parameter model to the amplification curve and extracts the coefficient, which describes the slope.

Usage

hookregNL(x, y, plot = FALSE, level = 0.995, simple = TRUE, manualtrim = 5)

Value

gives a numeric (S3 class, type of double) as output for the detection of a hook

Arguments

x

is the cycle numbers (x-axis).

y

is the cycle dependent fluorescence amplitude (y-axis).

plot

is a logical parameter indicating if the data should be plotted, Default: FALSE.

level

the confidence level required, Default: 0.99.

simple

is a logical parameter. If TRUE (default) only the slope, confidence interval and decisions are shown as output

manualtrim

is the number of cycles that should be removed from the background. (data.frame). If FALSE, a list including the 6-parameter model is the output.

Author

Andrej-Nikolai Spiess, Stefan Roediger, Michal Burdukiewcz

References

K. Barratt, J.F. Mackay, Improving Real-Time PCR Genotyping Assays by Asymmetric Amplification, J. Clin. Microbiol. 40 (2002) 1571--1572. doi:10.1128/JCM.40.4.1571-1572.2002.

Examples

library(qpcR)

# Analyze data from the boggy data set for potential hook effect like
# curvature
# has hook
res <- hookregNL(boggy[, 1], boggy[, 2])
res

# has no hook
res <- hookregNL(boggy[, 1], boggy[, 12])
res