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qpcR (version 1.2-4)

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).

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Version

Install

install.packages('qpcR')

Monthly Downloads

239

Version

1.2-4

License

GPL (>= 2)

Maintainer

Andrej-Nikolai Spiess

Last Published

January 26th, 2010

Functions in qpcR (1.2-4)

Calculation of qPCR efficiency by dilution curve analysis with an optional iterative search of the optimal threshold border

A qPCR dilution experiment with replicates (Lightcycler 480) from Guescini et al

Root-mean-squared-error of a fitted model

Calculation of PCR efficiency by the window-of-linearity method

Create nonlinear models from a dataframe and coerce them into a list

Function for qPCR model fitting

qPCR dilution experiment with replicates and different runs from Rutledge et al (Biorad Opticon)

Building a model which averages a batch of qPCR curves

Another qPCR dilution experiment with replicates (Roche Lightcycler)

PCR data from 15 different testicular biopsies (Roche Lightcycler)

Bayesian Information Criterion

Residual variance of a fitted model

Selection of the best model by nested F-tests/likelihood ratios/Akaike weights

Allen's PRESS (Prediction Sum-Of-Squares) statistic, aka P-square

Batch calculation of qPCR efficiency and several other important qPCR parameters with different methods

Calculation of ratios/propagated errors/confidence intervals/permutation p-values from qPCR runs with/without reference data

Akaike's second-order corrected Information Criterion for small sample sizes

A qPCR experiment with replicates and simulated inhibition (Lightcycler 480) from Guescini et al

Residual sum-of-squares of a fitted model

A qPCR dilution experiment with replicates (Stratagene MXPro3000P)

A residuals bar-plot with colour-coded bars

Evidence ratio for model comparison with AIC or AICc

The amplification efficiency curve of a fitted object

Calculation of PCR efficiency by fitting an exponential model

Comparison of all available sigmodal models by RMSE within the exponential region

Summarize measures for the goodness-of-fit

Combinatorial elimination of plateau and ground phase cycles

Plotting qPCR data with fitted curves/confidence bands/error bars

R-square value of a fitted model

Simple qPCR data import function (i.e. from text files or clipboard).

Calculation of Akaike weights/relative likelihoods/delta-AICs

General error analysis function using Monte-Carlo simulation/permutation/(first-order) error propagation

qPCR dilution experiment with replicates (Roche Lightcycler)

Calculation of qPCR efficiency and several other important qPCR parameters