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qpcR (version 1.2-0)

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

1.2-0

License

GPL (>= 2)

Maintainer

Andrej-Nikolai Spiess

Last Published

July 21st, 2009

Functions in qpcR (1.2-0)

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

Allen's PRESS (Prediction Sum-Of-Squares) statistic

Residual sum-of-squares of a fitted model

Summarize measures for the goodness-of-fit

R-square value of a fitted model

Evidence ratio for model comparison with AIC or AICc

Combinatorial elimination of plateau and ground phase cycles

The amplification efficiency curve of a fitted object

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

Another qPCR dilution experiment with replicates (Roche Lightcycler)

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

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

Building a model which averages a batch of qPCR curves

Calculation of PCR efficiency by fitting an exponential model

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

Plotting qPCR data with fitted curves/confidence bands

Residual variance of a fitted model

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

A qPCR dilution experiment with replicates (Stratagene MXPro3000P)

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

Calculation of qPCR efficiency and several other important qPCR parameters

PCR data from 15 different testicular biopsies (Roche Lightcycler)

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

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

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

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

qPCR dilution experiment with replicates (Roche Lightcycler)

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

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

Root-mean-squared-error of a fitted model

Function for qPCR model fitting

Calculation of Akaike weights/relative likelihoods/delta-AICs

A residuals bar-plot with colour-coded bars