hookregNL | R Documentation |
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)
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.
( |
gives a numeric
(S3 class, type of double
) as output
for the detection of a hook
Andrej-Nikolai Spiess, Stefan Roediger, Michal Burdukiewcz
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.
pcrfit
confint
# 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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