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qpcR (version 1.1-8)

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

1.1-8

License

GPL (>= 2)

Maintainer

Andrej-Nikolai Spiess

Last Published

March 27th, 2009

Functions in qpcR (1.1-8)

propagate

General error propagation function using covariates and Monte Carlo simulations
guescini1

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

Calculation of Akaike weights/relative likelihoods/delta-AICs
guescini2

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

Building a model which averages a batch of qPCR curves
evidence

Evidence ratio for model comparison with AIC or AICc
confband

Confidence bands for a sigmoidal fit
ratioplot

Plot method for data of class 'ratiocalc' which displays barplots of ratios with error bars
efficiency

Calculation of qPCR efficiency and several other important qPCR parameters
LR

Calculation of likelihood ratios for nested models
expfit

Calculation of PCR efficiency by fitting an exponential model
pcrplot

Plotting PCR data with fitted curves
rutledge

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

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

Root-mean-squared-error of a fitted model
AICc

Akaike's second-order corrected Information Criterion for small sample sizes
pcropt1

Combinatorial elimination of plateau and ground phase cycles
pcrGOF

Summarize measures for the goodness-of-fit
pcrfit

Simple wrapper function for fast model fitting
reps

qPCR dilution experiment with replicates (Roche Lightcycler)
mchoice

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

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

A residuals bar-plot with colour-coded bars
reps2

Another qPCR dilution experiment with replicates (Roche Lightcycler)
expcomp

Comparison of several sigmodal models by RMSE within the exponential region
reps3

A qPCR dilution experiment with replicates (Stratagene MXPro3000P)
PRESS

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

Formatting of PCR data with or without replicates for analysis
ratiocalc

Calculation of ratios/propagated errors/t-statistics for all permutations/combinations of qPCR runs with or without reference data
S27

PCR data from 15 different testicular biopsies (Roche Lightcycler)
eff

The amplification efficiency curve of a fitted object
RSS

Residual sum-of-squares of a fitted model
sliwin

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

Calculation of qPCR efficiency by dilution curve analysis
pcrimport

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

Residual variance of a fitted model
Rsq

R-square value of a fitted model
pcrpred

Value prediction from a fitted sigmoidal model