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qpcR (version 1.4-1)

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

1,795

Version

1.4-1

License

GPL (>= 2)

Last Published

June 14th, 2018

Functions in qpcR (1.4-1)

fitchisq

The chi-square goodness-of-fit
pcrsim

Simulation of sigmoidal qPCR data with goodness-of-fit analysis
replist

Amalgamation of single data models into a model containing replicates
mselect

Sigmoidal model selection by different criteria
plot.pcrfit

Plotting qPCR data with fitted curves
llratio

Calculation of likelihood ratios for nested models
pcrimport2

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

Calculation of qPCR efficiency by the 'window-of-linearity' method
refmean

Averaging of multiple reference genes
modlist

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

Calculation of the 'midpoint' region
pcropt1

Combinatorial elimination of plateau and ground phase cycles
takeoff

Calculation of the qPCR takeoff point
meltcurve

Melting curve analysis with (iterative) Tm identification and peak area calculation/cutoff
parKOD

Parameters that can be changed to tweak the kinetic outlier methods
pcrfit

Workhorse function for qPCR model fitting
maxRatio

The maxRatio method as in Shain et al. (2008)
pcrGOF

Summarize measures for the goodness-of-fit
pcrboot

Bootstrapping and jackknifing qPCR data
pcrbatch

Batch calculation of qPCR efficiency and other qPCR parameters
predict.pcrfit

Value prediction from a fitted qPCR model
qpcR.news

Display news and changes of qpcR package versions
propagate

Error propagation using different methods
qpcR_functions

The nonlinear/mechanistic models implemented in qpcR
ratioPar

Calculation of ratios in a batch format from external PCR parameters
resplot

An (overlayed) residuals barplot
resVar

Residual variance of a fitted model
update.pcrfit

Updating and refitting a qPCR model
pcrimport

Advanced qPCR data import function
qpcR_datasets

The (published) datasets implemented in qpcR
ratiobatch

Calculation of ratios in a batch format for multiple genes/samples
ratiocalc

Calculation of ratios from qPCR runs with/without reference genes
RSS

Residual sum-of-squares of a fitted model
KOD

(K)inetic (O)utlier (D)etection using several methods
LRE

Calculation of qPCR efficiency by the 'linear regression of efficiency' method
Rsq.ad

Adjusted R-square value of a fitted model
Rsq

R-square value of a fitted model
Cy0

Cy0 alternative to threshold cycles as in Guescini et al. (2008)
RMSE

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

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

Calculation of Akaike weights/relative likelihoods/delta-AICs
LOF.test

Formal lack-Of-Fit test of a nonlinear model against a one-way ANOVA model
AICc

Akaike's second-order corrected Information Criterion
expfit

Calculation of PCR efficiency by fitting an exponential model
eff

The amplification efficiency curve of a fitted object
calib

Calculation of qPCR efficiency using dilution curves and replicate bootstrapping
expcomp

Comparison of all sigmodal models within the exponential region
is.outlier

Outlier summary for objects of class 'modlist' or 'replist'
evidence

Evidence ratio for model comparisons with AIC, AICc or BIC
getPar

Batch calculation of qPCR fit parameters/efficiencies/threshold cycles with simple output, especially tailored to high-throughput data
efficiency

Calculation of qPCR efficiency and other important qPCR parameters