Modelling and analysis of real-time PCR data

[Up] [Top]

Documentation for package ‘qpcR’ version 1.3-6

Help Pages

AICc Akaike's second-order corrected Information Criterion
akaike.weights Calculation of Akaike weights/relative likelihoods/delta-AICs
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 qPCR dilution experiments from Batsch et al. (2008)
batsch2 qPCR dilution experiments from Batsch et al. (2008)
batsch3 qPCR dilution experiments from Batsch et al. (2008)
batsch4 qPCR dilution experiments from Batsch et al. (2008)
batsch5 qPCR dilution experiments from Batsch et al. (2008)
boggy qPCR dilution experiments from Boggy et al. (2010)
calib Calculation of qPCR efficiency by dilution curve analysis
calib2 Calculation of qPCR efficiency by dilution curve bootstrapping
chag The nonlinear/mechanistic models 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)
dyemelt Melting curves of a 4-plex qPCR with different fluorescence dyes
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
fitchisq The chi-square goodness-of-fit
getPar Batch calculation of qPCR fit parameters/efficiencies/threshold cycles with simple output, especially tailored to high-throughput data
guescini1 qPCR dilution experiments from Guescini et al. (2008)
guescini2 qPCR dilution experiments from Guescini et al. (2008)
HQIC Hannan-Quinn Information Criterion
htPCR High throughput qPCR experiment with 8858 runs
is.outlier Outlier summary for objects of class 'modlist' or 'replist'
KOD (K)inetic (O)utlier (D)etection using several methods
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 qPCR dilution and inhibition data from Lievens et al. (2012)
lievens2 qPCR dilution and inhibition data from Lievens et al. (2012)
lievens3 qPCR dilution and inhibition data from Lievens et al. (2012)
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
mak2 The nonlinear/mechanistic models implemented in qpcR
mak3 The nonlinear/mechanistic models implemented in qpcR
mak3n 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
neill.test Neill's lack-of-fit test when replicates are lacking
parKOD Parameters that can be changed to tweak the kinetic outlier methods
parMAK Parameters that can be changed to tweak the mak2/mak3 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
qpcR.news Display news and changes of qpcR package versions
ratiobatch Calculation of ratios in a batch format for multiple genes/samples
ratiocalc Calculation of ratios from qPCR runs with/without reference genes
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 qPCR dilution experiments from the package author
reps2 qPCR dilution experiments from the package author
reps3 qPCR dilution experiments from the package author
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 qPCR dilution experiments from Rutledge (2004)
S27 qPCR data of the S27a transcript in 15 testicular biopsies
sliwin Calculation of qPCR efficiency by the 'window-of-linearity' method
takeoff Calculation of the qPCR takeoff point
testdat dataset with noisy data to provoke fitting errors
update.pcrfit Updating and refitting a qPCR model
vermeulen1 A large-scale qPCR dataset from Vermeulen et al. (2009)
vermeulen2 A large-scale qPCR dataset from Vermeulen et al. (2009)