qpcR: Modelling and analysis of real-time PCR data
Description
Model fitting, optimal model selection and calculation of various features that are essential
in the analysis of quantitative real-time polymerase chain reaction (qPCR).Details
ll{
Package: qpcR
Type: Package
LazyLoad: yes
LazyData: yes
Version: 1.1-7
License: GNU GPL (version 2 or any later version)
Depends: R (>= 2.0.0), drc
URL: http://www.dr-spiess.de; http://www.r-project.org; http://www.bioassay.dk
Packaged: Nov 10 2008; spiess
Built: R 2.8.0; ; 2008-11-10; windows
}
package:
qpcR Modelling and analysis of real-time PCR data.
Functions:
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.
mchoice Selection of the best model by nested F-tests, likelihood ratios or Akaike weights.
pcrplot Plotting PCR data with fitted curves.
repform Formatting of PCR data with or without replicates for analysis.
resVar Residual variance of a fitted model.
Rsq R-square value of a fitted model.
sliwin Calculation of PCR efficiency by the window-of-linearity method.
expfit Calculation of PCR efficiency by fitting an exponential model.
pcrbatch Batch calculation of qPCR efficiency and several other important qPCR parameters.
RMSE Root-mean-squared-error of a fitted model.
calib Calculation of qPCR efficiency by dilution curve analysis.
pcrpred Value prediction from a fitted sigmoidal model.
pcrGOF Summarize measures for the goodness-of-fit.
expcomp Comparison of several sigmodal models by RMSE within the exponential region.
pcrimport Simple qPCR data import function (i.e. from text files, clipboard).
pcrfit Simple wrapper function for fast model fitting.
AICc Akaike's second-order corrected Information Criterion for small sample sizes.
evidence Evidence ratio for model comparison with AIC or AICc.
modlist Create nonlinear models from a dataframe and coerce them into a list.
pcropt1 Combinatorial elimination of plateau and ground phase cycles.
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.
curvemean Building a model which averages a batch of qPCR curves.
PRESS Allen's PRESS (Prediction Sum-Of-Squares) statistic.
akaike.weights Calculation of Akaike weights/relative likelihoods/delta-AICs.
LR Calculation of likelihood ratios for nested models.
RSS Residual sum-of-squares of a fitted model.
residplot A residuals bar-plot with colour-coded bars.
Cy0 Cy0 alternative to crossing points/threshold cycles as in Guescini et al.
maxRatio The maxRatio method as in Shain et al.
Datasets:
reps qPCR dilution experiment with replicates (Roche Lightcycler).
reps2 Another qPCR dilution experiment with replicates (Roche Lightcycler).
rutledge qPCR data from Rutledge et al (Biorad Opticon).
S27 qPCR data from 15 different testicular biopsies (Roche Lightcycler).
reps3 A qPCR dilution experiment with replicates (Stratagene MXPro3000P).
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.