Modelling and analysis of real-time PCR data

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Documentation for package ‘qpcR’ version 1.3-7.1

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A B C D E F G H I K L M N P Q R S T U V

-- A --

AICc Akaike's second-order corrected Information Criterion
akaike.weights Calculation of Akaike weights/relative likelihoods/delta-AICs

-- B --

b3 The nonlinear/mechanistic models implemented in qpcR
b4 The nonlinear/mechanistic models implemented in qpcR
b5 The nonlinear/mechanistic models implemented in qpcR
b6 The nonlinear/mechanistic models implemented in qpcR
b7 The nonlinear/mechanistic models implemented in qpcR
batchstat Concatenating or calculating statistics on a 'pcrbatch'
batsch1 The (published) datasets implemented in qpcR
batsch2 The (published) datasets implemented in qpcR
batsch3 The (published) datasets implemented in qpcR
batsch4 The (published) datasets implemented in qpcR
batsch5 The (published) datasets implemented in qpcR
boggy The (published) datasets implemented in qpcR

-- C --

calib Calculation of qPCR efficiency by dilution curve analysis
calib2 Calculation of qPCR efficiency by dilution curve bootstrapping
cm3 The nonlinear/mechanistic models implemented in qpcR
competimer The (published) datasets implemented in qpcR
curvemean Building a model which averages a batch of qPCR curves
Cy0 Cy0 alternative to threshold cycles as in Guescini et al. (2008)

-- D --

dil4reps94 The (published) datasets implemented in qpcR
dyemelt The (published) datasets implemented in qpcR

-- E --

eff The amplification efficiency curve of a fitted object
efficiency Calculation of qPCR efficiency and other important qPCR parameters
evidence Evidence ratio for model comparisons with AIC, AICc or BIC
expcomp Comparison of all sigmodal models within the exponential region
expfit Calculation of PCR efficiency by fitting an exponential model
expGrowth The nonlinear/mechanistic models implemented in qpcR

-- F --

fitchisq The chi-square goodness-of-fit

-- G --

getPar Batch calculation of qPCR fit parameters/efficiencies/threshold cycles with simple output, especially tailored to high-throughput data
guescini1 The (published) datasets implemented in qpcR
guescini2 The (published) datasets implemented in qpcR

-- H --

HQIC Hannan-Quinn Information Criterion
htPCR The (published) datasets implemented in qpcR

-- I --

is.outlier Outlier summary for objects of class 'modlist' or 'replist'

-- K --

karlen1 The (published) datasets implemented in qpcR
karlen2 The (published) datasets implemented in qpcR
karlen3 The (published) datasets implemented in qpcR
KOD (K)inetic (O)utlier (D)etection using several methods

-- L --

l3 The nonlinear/mechanistic models implemented in qpcR
l4 The nonlinear/mechanistic models implemented in qpcR
l5 The nonlinear/mechanistic models implemented in qpcR
l6 The nonlinear/mechanistic models implemented in qpcR
l7 The nonlinear/mechanistic models implemented in qpcR
lievens1 The (published) datasets implemented in qpcR
lievens2 The (published) datasets implemented in qpcR
lievens3 The (published) datasets implemented in qpcR
lin2 The nonlinear/mechanistic models implemented in qpcR
linexp The nonlinear/mechanistic models implemented in qpcR
llratio Calculation of likelihood ratios for nested models
LOF.test Formal lack-Of-Fit test of a nonlinear model against a one-way ANOVA model
LRE Calculation of qPCR efficiency by the 'linear regression of efficiency' method

-- M --

mak2 The nonlinear/mechanistic models implemented in qpcR
mak2i The nonlinear/mechanistic models implemented in qpcR
mak3 The nonlinear/mechanistic models implemented in qpcR
mak3i The nonlinear/mechanistic models implemented in qpcR
maxRatio The maxRatio method as in Shain et al. (2008)
meanlist Amalgamation of single data models into an averaged model
meltcurve Melting curve analysis with (iterative) Tm identification and peak area calculation/cutoff
midpoint Calculation of the 'midpoint' region
modlist Create nonlinear models from a dataframe and coerce them into a list
mselect Sigmoidal model selection by different criteria

-- N --

neill.test Neill's lack-of-fit test when replicates are lacking

-- P --

parKOD Parameters that can be changed to tweak the kinetic outlier methods
pcrbatch Batch calculation of qPCR efficiency and other qPCR parameters
pcrboot Bootstrapping and jackknifing qPCR data
pcrfit Workhorse function for qPCR model fitting
pcrGOF Summarize measures for the goodness-of-fit
pcrimport Advanced qPCR data import function
pcrimport2 Simple qPCR data import function (i.e. from text files or clipboard)
pcropt1 Combinatorial elimination of plateau and ground phase cycles
pcropt2 Elimination of qPCR cycles with low/high impact on fitted parameters
pcrsim Simulation of sigmoidal qPCR data with goodness-of-fit analysis
plot.pcrfit Plotting qPCR data with fitted curves/confidence bands/error bars
predict.pcrfit Value prediction from a fitted qPCR model
PRESS Allen's PRESS (Prediction Sum-Of-Squares) statistic, aka P-square
propagate General error analysis function using different methods

-- Q --

qpcR.news Display news and changes of qpcR package versions

-- R --

ratiobatch Calculation of ratios in a batch format for multiple genes/samples
ratiocalc Calculation of ratios from qPCR runs with/without reference genes
ratioPar Calculation of ratios in a batch format from external PCR parameters
refmean Averaging of multiple reference genes
rep2mod Converts a 'replist' back to a 'modlist'
replist Amalgamation of single data models into a model containing replicates
reps The (published) datasets implemented in qpcR
reps2 The (published) datasets implemented in qpcR
reps3 The (published) datasets implemented in qpcR
reps384 The (published) datasets implemented in qpcR
resplot An (overlayed) residuals barplot
resVar Residual variance of a fitted model
RMSE Root-mean-squared-error of a fitted model
Rsq R-square value of a fitted model
Rsq.ad Adjusted R-square value of a fitted model
RSS Residual sum-of-squares of a fitted model
rutledge The (published) datasets implemented in qpcR

-- S --

S27 qPCR data of the S27a transcript in 15 testicular biopsies
sliwin Calculation of qPCR efficiency by the 'window-of-linearity' method
spl3 The nonlinear/mechanistic models implemented in qpcR

-- T --

takeoff Calculation of the qPCR takeoff point
testdat The (published) datasets implemented in qpcR

-- U --

update.pcrfit Updating and refitting a qPCR model

-- V --

vermeulen1 The (published) datasets implemented in qpcR
vermeulen2 The (published) datasets implemented in qpcR