The qpcR Package - NexTag Supports Open Source Initiatives

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12 expcompExamples### compare two models, four-parameter and five-parameterm1
expfit 13expfitCalculation of PCR efficiency by fitting of an exponential model andminimization of residual varianceDescriptionUsageAn exponential model is fit to a sliding window of defined size along the qPCR data. In the windowwith minimal residual variance (or minimal AIC), the efficiency is calculated.ArgumentsDetailsValueexpfit(object, fitcyc = 5, plot = TRUE, crit = "resVar", start = 5, maxeff = 2, mobjecta ’drc’ object.fitcyc the size of the sliding window, default is 5.plotcritif TRUE the result is plotted, if FALSE the result is diplayed on the console.the criterium to be minimized. Either "resVar" or "AICc".start the cycle number to start from. Defaults to 5.maxeffmineffthe maximum allowed efficiency of the fit.the minimum allowed efficiency of the fit. See Details.The exponential growth function f(x) = b ∗ exp(k ∗ x) + e is fit to the data. To avoid good fitsin the plateau phase, the fitting procedure is stopped at cpD1 (first derivative maximum cycle). Theefficiency is calculated a) from the exponential fit with E = exp(d) (Eff.fit) and b) for each cyclewithin the exponential region from the raw fluorescence values by E =F (n)F (n−1) (Eff.curve).The inital template fluorescence (F0) is derived from parameter b. Avoiding good fits in the noisyground phase can be tweaked by increasing the effmin parameter.A list with the following components:cyc.bestEff.fitEff.curveresVarAICRMSEinitmodthe ’best’ cycle with the minimized criterium.the PCR efficiency calculated from the exponential fit.the PCR efficiency for each cycle within the exponential phase. See Details.the residual variance at the best cycle.the AIC at the best cycle.the root-mean-squared error at the best cycle.the initial template fluorescence, i.e. ’F0’.the exponential model from the best fit.
Page 1 and 2: The qpcR PackageFebruary 16, 2008Ty
Page 3 and 4: RMSE 3Author(s)Andrej-Nikolai Spies
Page 5 and 6: calib 5DetailsThe real-time PCR was
Page 7 and 8: confband 7Examples###define dilutio
Page 9 and 10: efficiency 9Examplesm
Page 11: evidence 11efficiency(m2, type = "m
Page 15 and 16: mchoice 15ValueA list with the foll
Page 17 and 18: pcrGOF 17DetailsValueFor a more det
Page 19 and 20: pcrfit 19DetailsValueThe qPCR raw d
Page 21 and 22: pcropt1 21Argumentsfilesepheaderquo
Page 23 and 24: pcrplot 23pcrplotPlotting PCR data
Page 25 and 26: qpcR 25Usagepcrpred(object, newdata
Page 27 and 28: epform 27confband qPCR data from Ru
Page 29 and 30: eps2 29Examplesdata(reps)### on sin
Page 31 and 32: esVar 31resVarResidual variance of
Page 33 and 34: sliwin 33DetailsValueTo avoid fits
Page 35: INDEX 35mchoice, 15modlist, 16multd

The qpcR Package - NexTag Supports Open Source Initiatives

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