is.outlier
(Package: qpcR) :
Outlier summary for objects of class 'modlist' or 'replist'
For model lists of class 'modlist' or 'replist', is.outlier returns a vector of logicals for each run if they are outliers (i.e. sigmoidal or kinetic) or not.
● Data Source:
CranContrib
● Keywords: models, nonlinear
● Alias: is.outlier
●
0 images
|
calib
(Package: qpcR) :
Calculation of qPCR efficiency using dilution curves and replicate bootstrapping
This function calculates the PCR efficiency from a classical qPCR dilution experiment. The threshold cycles are plotted against the logarithmized concentration (or dilution) values, a linear regression line is fit and the efficiency calculated by E = 10^{frac{-1}{slope}}. A graph is displayed with the raw values plotted with the threshold cycle and the linear regression curve. The threshold cycles are calculated either by some arbitrary fluorescence value (i.e. as given by the qPCR software) or calculated from the second derivative maximum of the dilution curves. If values to be predicted are given, they are calculated from the curve and also displayed within. calib2 uses a bootstrap approach if replicates for the dilutions are supplied. See 'Details'.
● Data Source:
CranContrib
● Keywords: models, nonlinear
● Alias: calib
●
0 images
|
pcrGOF
(Package: qpcR) :
Summarize measures for the goodness-of-fit
Calculates all implemented measures for the goodness-of-fit and returns them as a list. Works for objects of class pcrfit, lm, glm, nls, drc and many others...
● Data Source:
CranContrib
● Keywords: models, nonlinear
● Alias: pcrGOF
●
0 images
|
maxRatio
(Package: qpcR) :
The maxRatio method as in Shain et al. (2008)
The maximum ratio (MR) is determined along the cubic spline interpolated curve of frac{F_n}{F_{n-1}} and the corresponding cycle numbers FCN and its adjusted version FCNA are then calculated for MR.
● Data Source:
CranContrib
● Keywords: models, nonlinear
● Alias: maxRatio
●
0 images
|
akaike.weights
(Package: qpcR) :
Calculation of Akaike weights/relative likelihoods/delta-AICs
Calculates Akaike weights from a vector of AIC values.
● Data Source:
CranContrib
● Keywords: models, nonlinear
● Alias: akaike.weights
●
0 images
|
Cy0
(Package: qpcR) :
Cy0 alternative to threshold cycles as in Guescini et al. (2008)
An alternative to the classical crossing point/threshold cycle estimation as described in Guescini et al (2002). A tangent is fit to the first derivative maximum (point of inflection) of the modeled curve and the intersection with the x-axis is calculated.
● Data Source:
CranContrib
● Keywords: models, nonlinear
● Alias: Cy0
●
0 images
|
pcrfit
(Package: qpcR) :
Workhorse function for qPCR model fitting
This is the workhorse function of the qpcR package that fits one of the available models to qPCR data using (weighted) nonlinear least-squares (Levenberg-Marquardt) fitting from nlsLM of the 'minpack.lm' package.
● Data Source:
CranContrib
● Keywords: models, nonlinear
● Alias: pcrfit
●
0 images
|
pcrboot
(Package: qpcR) :
Bootstrapping and jackknifing qPCR data
Confidence intervals for the estimated parameters and goodness-of-fit measures are calculated for a nonlinear qPCR data fit by either
a) boostrapping the residuals of the fit or
b) jackknifing and refitting the data.
● Data Source:
CranContrib
● Keywords: models, nonlinear
● Alias: pcrboot
●
0 images
|
LOF.test
(Package: qpcR) :
Formal lack-Of-Fit test of a nonlinear model against a one-way ANOVA model
Tests the nonlinear model against a more general one-way ANOVA model and from a likelihood ratio test. P-values are derived from the F- and χ^2 distribution, respectively.
● Data Source:
CranContrib
● Keywords: models, nonlinear
● Alias: LOF.test
●
0 images
|
expfit
(Package: qpcR) :
Calculation of PCR efficiency by fitting an exponential model
An exponential model is fit to a window of defined size on the qPCR raw data. The window is identified either by the second derivative maximum 'cpD2' (default), 'studentized outlier' method as described in Tichopad et al. (2003), the 'midpoint' method (Peirson et al., 2003) or by subtracting the difference of cpD1 and cpD2 from cpD2 ('ERBCP', unpublished).
● Data Source:
CranContrib
● Keywords: models, nonlinear
● Alias: expfit
●
0 images
|
providing 
.