Modelling and analysis of real-time PCR data

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Documentation for package ‘qpcR’ version 1.1-8

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AICc Akaike's second-order corrected Information Criterion for small sample sizes
akaike.weights Calculation of Akaike weights/relative likelihoods/delta-AICs
calib Calculation of qPCR efficiency by dilution curve analysis
calib2 Calculation of qPCR efficiency by dilution curve analysis and an iterative search of the optimal threshold border
confband Confidence bands for a sigmoidal fit
curvemean Building a model which averages a batch of qPCR curves
Cy0 Cy0 alternative to crossing points/threshold cycles as in Guescini et al
drmfit The drm fitting engine, replicated to the qpcR package
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 an exponential model
guescini1 A qPCR dilution experiment with replicates (Lightcycler 480) from Guescini et al
guescini2 A qPCR experiment with replicates and simulated inhibition (Lightcycler 480) from Guescini et al
LR Calculation of likelihood ratios for nested models
maxRatio The maxRatio method as in Shain et al
mchoice Selection of the best model by nested F-tests/likelihood ratios/Akaike weights
modlist Create nonlinear 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 Combinatorial elimination of plateau and ground phase cycles
pcrplot Plotting PCR data with fitted curves
pcrpred Value prediction from a fitted sigmoidal model
PRESS Allen's PRESS (Prediction Sum-Of-Squares) statistic
propagate General error propagation function using covariates and Monte Carlo simulations
ratiocalc Calculation of ratios/propagated errors/t-statistics for all permutations/combinations of qPCR runs with or without reference data
ratioplot Plot method for data of class 'ratiocalc' which displays barplots of ratios with error bars
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)
residplot A residuals bar-plot with colour-coded bars
REST qpcR implementation of the popular REST software
resVar Residual variance of a fitted model
RMSE Root-mean-squared-error of a fitted model
Rsq R-square value of a fitted model
RSS Residual sum-of-squares of a fitted model
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