Modelling and analysis of real-time PCR data

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Documentation for package ‘qpcR’ version 1.0-6

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AICc Akaike's second-order Information Criterion for small sample numbers
calib Calculation of qPCR efficiency by dilution curve analysis
confband Confidence bands for a sigmoidal fit
eff The amplification efficiency curve of a fitted object
efficiency Calculation of qPCR efficiency and several other important qPCR parameters
evidence Evidence ratio for model comparison with AIC or AICc
expcomp Comparison of several sigmodal models by RMSE within the exponential region
expfit Calculation of PCR efficiency by fitting of an exponential model and minimization of residual variance
expfit2 Calculation of PCR efficiency by fitting of an exponential model after outlier cycle detection
mchoice Selection of the best model by nested F-tests
modlist Create sigmoidal models from a dataframe and coerce them into a list
pcrbatch Batch calculation of qPCR efficiency and several other important qPCR parameters with different methods
pcrfit Simple wrapper function for fast model fitting
pcrGOF Summarize measures for the goodness-of-fit
pcrimport Simple qPCR data import function (i.e. from text files or clipboard).
pcropt1 Optimization of efficiency and F0 estimation by combinatorial cycle elimination of plateau and ground phase cycles
pcrplot Plotting PCR data with fitted curves
pcrpred Value prediction from a fitted sigmoidal model
qpcR Modelling and analysis of real-time PCR data
repform Formatting of PCR data with or without replicates for analysis
reps qPCR dilution experiment with replicates (Roche Lightcycler)
reps2 Another qPCR dilution experiment with replicates (Roche Lightcycler)
reps3 A qPCR dilution experiment with replicates (Stratagene MXPro3000P)
resVar Residual variance of a sigmoidal fit
RMSE Root-mean-squared-error of a sigmoidal fit
Rsq R-square of a sigmoidal fit
rutledge qPCR dilution experiment with replicates and different runs from Rutledge et al (Biorad Opticon)
S27 PCR data from 15 different testicular biopsies (Roche Lightcycler)
sliwin Calculation of PCR efficiency by the window-of-linearity method