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qpcR (version 1.2-2)

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

1,227

Version

1.2-2

License

GPL (>= 2)

Maintainer

Andrej-Nikolai Spiess

Last Published

September 21st, 2009

Functions in qpcR (1.2-2)

Calculation of PCR efficiency by fitting an exponential model

R-square value of a fitted model

Evidence ratio for model comparison with AIC or AICc

Residual variance of a fitted model

Function for qPCR model fitting

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

A residuals bar-plot with colour-coded bars

Combinatorial elimination of plateau and ground phase cycles

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

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

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

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

Bayesian Information Criterion

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

Residual sum-of-squares of a fitted model

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

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

Calculation of qPCR efficiency and several other important qPCR parameters

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

Another qPCR dilution experiment with replicates (Roche Lightcycler)

PCR data from 15 different testicular biopsies (Roche Lightcycler)

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

Calculation of Akaike weights/relative likelihoods/delta-AICs

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

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

Root-mean-squared-error of a fitted model

Summarize measures for the goodness-of-fit

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

The amplification efficiency curve of a fitted object

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

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

Building a model which averages a batch of qPCR curves

qPCR dilution experiment with replicates (Roche Lightcycler)

A qPCR dilution experiment with replicates (Stratagene MXPro3000P)