qpcR {qpcR} | R Documentation |
Model fitting, optimal model selection and calculation of various features that are essential in the analysis of quantitative real-time polymerase chain reaction (qPCR).
Package: | qpcR |
Type: | Package |
LazyLoad: | yes |
LazyData: | yes |
Version: | 1.0-6 |
Date: | 2008-01-28 |
License: | GNU GPL (version 2 or any later version) |
Depends: | R (>= 2.0.0), drc |
URL: | http://www.r-project.org; http://www.bioassay.dk; http://www.dr-spiess.de |
Packaged: | Thu Jan 17 2008; spiess |
Built: | R 2.6.0; ; 2008-01-28; windows |
Index:
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. pcrplot Plotting PCR data with fitted curves. repform Formatting of PCR data with or without replicates for analysis. resVar Residual variance of a sigmoidal fit. Rsq R-square value of a sigmoidal fit. sliwin Calculation of PCR efficiency by the window-of-linearity method. 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 and outlier cycle detection. pcrbatch Batch calculation of qPCR efficiency and several other important qPCR parameters. RMSE Root-mean-squared-error of a sigmoidal fit. 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 Information Criterion for small sample numbers. evidence Evidence ratio for model comparison with AIC or AICc. modlist Create sigmoidal models from a dataframe and coerce them into a list. pcropt1 Optimization of efficiency and F0 estimation by combinatorial cycle elimination of plateau and ground phase cycles. 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).
Andrej-Nikolai Spiess <a.spiess@uke.uni-hamburg.de>, Christian Ritz <ritz@kvl.dk>
Maintainer: Andrej-Nikolai Spiess <a.spiess@uke.uni-hamburg.de>