maxRatio {qpcR} | R Documentation |
The maxRatio method as in Shain et al. (2008)
Description
The maximum ratio (MR) is determined along the cubic spline interpolated curve of and the corresponding cycle numbers FCN and its adjusted version FCNA are then calculated for MR.
Usage
maxRatio(x, method = c("spline", "sigfit"), baseshift = NULL,
smooth = TRUE, plot = TRUE, ...)
Arguments
x |
an object of class 'pcrfit' (single run) or 'modlist' (multiple runs). |
method |
the parameters are either calculated from the cubic spline interpolation (default) or a sigmoidal fit. |
baseshift |
numerical. Shift value in case of |
smooth |
logical. If |
plot |
Should diagnostic plots be displayed? |
... |
Details
In a first step, the raw fluorescence data can be smoothed by a 5-point convolution filter. This is optional but feasible for many qPCR setups with significant noise in the baseline region, and therefore set to TRUE
as default. If baseshift
is a numeric value, this is added to each response value (baseline shifting). Finally, a cubic spline is fit with a resolution of 0.01 cycles and the maximum ratio (efficiency) is calculated by
.
is then calculated as the cycle number at
and from this the adjusted
. Sometimes problems are encountered in which, due to high noise in the background region, randomly high efficiency ratios are calculated. This must be resolved by tweaking the
baseshift
value.
Value
A list with the following components:
eff |
the maximum efficiency. Equals to |
mr |
the maximum ratio. |
fcn |
the cycle number at |
fcna |
an adjusted |
names |
the names of the runs as taken from the original dataframe. |
Note
This function has been approved by the original author (Eric Shain).
Author(s)
Andrej-Nikolai Spiess
References
A new method for robust quantitative and qualitative analysis of real-time PCR.
Shain EB & Clemens JM.
Nucleic Acids Research (2008), 36: e91.
Examples
## On single curve using baseline shifting.
m1 <- pcrfit(reps, 1, 2, l5)
maxRatio(m1, baseshift = 0.3)
## On a 'modlist' using baseline shifting.
## Not run:
ml1 <- modlist(reps, model = l5)
maxRatio(ml1, baseshift = 0.5)
## End(Not run)