hookregNL: hookregNL - A function to calculate the slope of...

In PCRedux: Quantitative Polymerase Chain Reaction (qPCR) Data Mining and Machine Learning Toolkit

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)

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.

Value

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

Author(s)

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.

See Also

pcrfit confint

Examples

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

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

PCRedux documentation built on May 11, 2022, 5:18 p.m.