Modelling and analysis of real-time PCR data

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Documentation for package ‘qpcR’ version 1.2-4

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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
b3 The nonlinear models implemented in qpcR
b4 The nonlinear models implemented in qpcR
b5 The nonlinear models implemented in qpcR
baro5 The nonlinear models implemented in qpcR
batchstat Concatenating or calculating statistics on a 'pcrbatch'
batsch1 qPCR dilution experiments with replicates (Lightcycler 1.0) from Batsch et al
batsch2 qPCR dilution experiments with replicates (Lightcycler 1.0) from Batsch et al
batsch3 qPCR dilution experiments with replicates (Lightcycler 1.0) from Batsch et al
batsch4 qPCR dilution experiments with replicates (Lightcycler 1.0) from Batsch et al
batsch5 qPCR dilution experiments with replicates (Lightcycler 1.0) from Batsch et al
BIC Bayesian Information Criterion
calib Calculation of qPCR efficiency by dilution curve analysis with an optional iterative search of the optimal threshold border
calib2 Calculation of qPCR efficiency by dilution curve analysis and bootstrapping of dilution curve replicates
curvemean Building a model which averages a batch of qPCR curves
Cy0 Cy0 alternative to crossing points/threshold cycles as in Guescini et al
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 all available sigmodal models by RMSE within the exponential region
expfit Calculation of PCR efficiency by fitting an exponential model
expGrowth The nonlinear models implemented in qpcR
fitprob The (chi-square) fit probability
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
l3 The nonlinear models implemented in qpcR
l4 The nonlinear models implemented in qpcR
l5 The nonlinear models implemented in qpcR
LR Calculation of likelihood ratios for nested models
maxRatio The maxRatio method as in Shain et al
meanlist Amalgamation of single data models to a model containing the averaged model
midpoint Calculation of the exponential region midpoint according to Peirson et al
modlist Create nonlinear models from a dataframe and coerce them into a list
mselect Selection of the best model by nested F-tests/likelihood ratios/Akaike weights
outlier Calculation of qPCR outlier cycles
pcrbatch Batch calculation of qPCR efficiency and several other important qPCR parameters with different methods
pcrboot Bootstrapping and jackknifing qPCR (and other) data
pcrfit Function for qPCR 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
pcropt2 Elimination of qPCR cycles with low (high) impact on fitted parameters
pcrsim Simulation of sigmoidal qPCR data with goodness-of-fit analysis for different models
plot.pcrfit Plotting qPCR data with fitted curves/confidence bands/error bars
predict.pcrfit Value prediction from a fitted qPCR model
PRESS Allen's PRESS (Prediction Sum-Of-Squares) statistic, aka P-square
propagate General error analysis function using Monte-Carlo simulation/permutation/(first-order) error propagation
ratiocalc Calculation of ratios/propagated errors/confidence intervals/permutation p-values from qPCR runs with/without reference data
replist Amalgamation of single data models to a model containing replicates
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)
resplot A residuals bar-plot with colour-coded bars
resVar Residual variance of a fitted model
RMSE Root-mean-squared-error of a fitted model
Rsq R-square value of a fitted model
Rsq.ad Adjusted R-square value of a fitted model
Rsq.cor R-square derived from correlation of data and fitted values
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
update.pcrfit Updating and refitting a qPCR model
w3 The nonlinear models implemented in qpcR
w4 The nonlinear models implemented in qpcR