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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.
hookregNL(x, y, plot = FALSE, level = 0.995, simple = TRUE, manualtrim = 5)is the cycle numbers (x-axis).
is the cycle dependent fluorescence amplitude (y-axis).
is a logical parameter indicating if the data should be plotted, Default: FALSE.
the confidence level required, Default: 0.99.
is a logical parameter. If TRUE (default) only the slope, confidence interval and decisions are shown as output
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.
gives a numeric (S3 class, type of double) as output
for the detection of a hook
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.
# NOT RUN {
# 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
# }
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