Modelling and analysis of real-time PCR data

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Documentation for package ‘qpcR’ version 1.3-2

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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
b6 The nonlinear models implemented in qpcR
baro5 The nonlinear models implemented in qpcR
baseline Baselining and refitting qPCR data based on six-parameter sigmoidal models
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
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
cbind.na Create data frames from objects of unequal size or combine R objects of unequal size by Rows or Columns
curvemean Building a model which averages a batch of qPCR curves
Cy0 Cy0 alternative to crossing points/threshold cycles as in Guescini et al
data.frame.na Create data frames from objects of unequal size or combine R objects of unequal size by Rows or Columns
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
fitchisq The chi-square goodness-of-fit
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
is.outlier Outlier summary for objects of class 'pcrfit, 'modlist' or 'replist'
KOD (K)inetic (O)utlier (D)etection according to Bar et al. (2003) or using Partitioning Around Medoids
l3 The nonlinear models implemented in qpcR
l4 The nonlinear models implemented in qpcR
l5 The nonlinear models implemented in qpcR
l6 The nonlinear models implemented in qpcR
LOF.test A formal Lack-Of-Fit test of a nonlinear model against a one-way ANOVA model
LR Calculation of likelihood ratios for nested models
maxRatio The maxRatio method as in Shain et al. (2008)
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/reduced chi-square
neill.test Neill's lack-of-fit test when replicates are lacking
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 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
qpcR.news Display news and changes of qpcR package versions
ratiobatch Calculation of ratios/propagated errors/confidence intervals/permutation p-values from qPCR runs with/without reference data in a batch format for multiple genes/samples
ratiocalc Calculation of ratios/propagated errors/confidence intervals/permutation p-values from qPCR runs with/without reference data
rbind.na Create data frames from objects of unequal size or combine R objects of unequal size by Rows or Columns
rep2mod Converts a 'replist' back to a 'modlist'
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
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)
sisti1 A qPCR dilution experiment with replicates (Lightcycler 480) from Sisti et al
sisti2 A qPCR dilution experiment with tannic acid as inhibitor (Lightcycler 480) from Sisti et al
sliwin Calculation of PCR efficiency by the window-of-linearity method
SOD (S)igmoidal (O)utlier (D)etection using first and second derivative maxima
update.pcrfit Updating and refitting a qPCR model
w3 The nonlinear models implemented in qpcR
w4 The nonlinear models implemented in qpcR