chipPCR: Toolkit of Helper Functions to Pre-Process Amplification Data

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A collection of functions to pre-process amplification curve data from polymerase chain reaction (PCR) or isothermal amplification reactions. Contains functions to normalize and baseline amplification curves, to detect both the start and end of an amplification reaction, several smoothers (e.g., LOWESS, moving average, cubic splines, Savitzky-Golay), a function to detect false positive amplification reactions and a function to determine the amplification efficiency. Quantification point (Cq) methods include the first (FDM) and second approximate derivative maximum (SDM) methods (calculated by a 5-point-stencil) and the cycle threshold method. Data sets of experimental nucleic acid amplification systems (VideoScan HCU, capillary convective PCR (ccPCR)) and commercial systems are included. Amplification curves were generated by helicase dependent amplification (HDA), ccPCR or PCR. As detection system intercalating dyes (EvaGreen, SYBR Green) and hydrolysis probes (TaqMan) were used.

Author
Stefan Roediger [cre, aut], Michal Burdukiewicz [aut], Konstantin A. Blagodatskikh [ctb]
Date of publication
2015-04-10 01:10:56
Maintainer
Stefan Roediger <stefan.roediger@hs-lausitz.de>
License
GPL-3
Version
0.0.8-10
URLs

View on CRAN

Man pages

AmpSim
Amplification curve simulator
AmpSim.gui
Amplification Curve Simulation Graphical User Interface
amptest-class
Class '"amptest"'
amptester
Amplification test
amptester.gui
Amplification Test Graphical User Interface
bg-class
Class '"bg"'
bg.max
Simple function to detect and correct the background range
C126EG595
qPCR Experiment for the Amplification of HPRT1 Using the...
C126EG685
qPCR Experiment for the Amplification of HPRT1 Using the...
C127EGHP
qPCR Experiment for the Amplification of MLC-2v Using the...
C17
Helicase Dependent Amplification of HPRT1 at Different...
C316.amp
qPCR Experiment for the Amplification of adk Using the...
C316.melt.hr
Melting Curves (resolution: 0.2 degrees Celsius / step) for...
C316.melt.lr
Melting Curves (resolution: 0.5 degrees Celsius / step) for...
C317.amp
qPCR Experiment for the Amplification of adk Using the...
C317.melt.hr
Melting Curves (resolution: 0.1 degrees Celsius / step) for...
C317.melt.lr
Melting Curves (resolution: 0.5 degrees Celsius / step) for...
C54
qPCR Experiment for the amplification of MLC-2v using the...
C60.amp
qPCR Experiment for the Amplification of MLC-2v and Vimentin...
C60.melt
Melt Curves MLC-2v and Vimentin for the qPCR Experiment...
C67
Helicase Dependent Amplification of HPRT1 with different...
C81
Helicase Dependent Amplification of pCNG1 using the VideoScan...
C85
Helicase Dependent Amplification of Vimentin using the...
capillaryPCR
capillary convective PCR
CD74
Quantitative PCR with a hydrolysis probe and DNA binding dye
CD75
Helicase Dependent Amplification in the VideoScan HCU
chipPCR.datasets
Overview for data sets of the 'chipPCR' package
chipPCR-package
Toolkit of functions to pre-process amplification data
CPP
Curve Pre-processor
der-class
Class '"der"'
Eff1000
Highly Replicate Number Amplification Curves
Eff625
Highly Replicate Number Amplification Curves
Eff750
Highly Replicate Number Amplification Curves
Eff875
Highly Replicate Number Amplification Curves
effcalc
Analysis of the amplification efficiency
eff-class
Class '"eff"'
fixNA
Impute missing values into a column of amplification data
humanrater
humanrater, a graphical interface to rate curves
inder
Interpolate derivatives
LAMP
real-time loop-mediated isothermal amplification (LAMP) by...
lm.coefs
Compute linear model coefficients
MFIaggr
Multiple comparison of the cycle dependent variance of the...
MFIaggr.gui
Multiple Comparison of the Cycle Dependent Variance -...
normalizer
Normalize data
plot-bg
Plot 'bg' objects
plotCurves
Plot Curves in an Orthogonal Matrix
plot-der
Plot 'der' objects
plot-eff
Plot 'eff' objects
plot-refMFI
Plot 'refMFI' objects
refMFI-class
Class '"refMFI"'
rounder
Round der objects
RPA
Recombinase polymerase amplification (RPA) by Lutz et...
smoother
Wrapper for Several Smoothers of Amplification Data
summary-bg
Summary 'bg' objects
summary-der
Summary 'der' objects
summary-refMFI
Summary 'refMFI' objects
th-class
Class '"th"'
th.cyc
Threshold Cycle
VIMCFX96_60
Amplification Reaction Using the Bio-Rad CFX96
VIMCFX96_69
Amplification Reaction Using the Bio-Rad CFX96
VIMCFX96_meltcurve
Melting Curve Measured with the Bio-Rad CFX96
VIMiQ5_595
Amplification Reaction Using the Bio-Rad iQ5
VIMiQ5_685
Amplification Reaction Using the Bio-Rad iQ5
VIMiQ5_melt
Melting Curve Measured with the Bio-Rad iQ5

Files in this package

chipPCR
chipPCR/inst
chipPCR/inst/AmpSim.gui
chipPCR/inst/AmpSim.gui/ui.R
chipPCR/inst/AmpSim.gui/server.R
chipPCR/inst/AmpSim.gui/readme.md
chipPCR/inst/AmpSim.gui/DESCRIPTION
chipPCR/inst/CITATION
chipPCR/inst/amptester.gui
chipPCR/inst/amptester.gui/ui.R
chipPCR/inst/amptester.gui/server.R
chipPCR/inst/amptester.gui/amptester_report.Rmd
chipPCR/inst/amptester.gui/DESCRIPTION
chipPCR/inst/MFIaggr.gui
chipPCR/inst/MFIaggr.gui/ui.R
chipPCR/inst/MFIaggr.gui/server.R
chipPCR/inst/MFIaggr.gui/readme.md
chipPCR/inst/MFIaggr.gui/refMFI_report.Rmd
chipPCR/inst/MFIaggr.gui/DESCRIPTION
chipPCR/inst/doc
chipPCR/inst/doc/chipPCR.pdf
chipPCR/inst/doc/chipPCR.Rnw
chipPCR/inst/doc/chipPCR.R
chipPCR/NAMESPACE
chipPCR/CHANGELOG
chipPCR/data
chipPCR/data/VIMiQ5_685.rda
chipPCR/data/C126EG685.rda
chipPCR/data/C81.rda
chipPCR/data/VIMCFX96_60.rda
chipPCR/data/C316.melt.hr.rda
chipPCR/data/C126EG595.rda
chipPCR/data/Eff1000.rda
chipPCR/data/CD74.rda
chipPCR/data/C127EGHP.rda
chipPCR/data/RPA.rda
chipPCR/data/C317.melt.lr.rda
chipPCR/data/C67.rda
chipPCR/data/C60.amp.rda
chipPCR/data/C316.amp.rda
chipPCR/data/C316.melt.lr.rda
chipPCR/data/VIMCFX96_69.rda
chipPCR/data/C60.melt.rda
chipPCR/data/VIMCFX96_meltcurve.rda
chipPCR/data/C85.rda
chipPCR/data/Eff625.rda
chipPCR/data/datalist
chipPCR/data/capillaryPCR.rda
chipPCR/data/VIMiQ5_595.rda
chipPCR/data/C17.rda
chipPCR/data/LAMP.rda
chipPCR/data/Eff750.rda
chipPCR/data/C317.amp.rda
chipPCR/data/CD75.rda
chipPCR/data/C54.rda
chipPCR/data/C317.melt.hr.rda
chipPCR/data/VIMiQ5_melt.rda
chipPCR/data/Eff875.rda
chipPCR/R
chipPCR/R/classes.R
chipPCR/R/smoother.R
chipPCR/R/rounder.R
chipPCR/R/CPP.R
chipPCR/R/amptester.R
chipPCR/R/humanrater.R
chipPCR/R/AmpSim.gui.R
chipPCR/R/lm.coefs.R
chipPCR/R/bg.max.R
chipPCR/R/amptester.gui.R
chipPCR/R/normalizer.R
chipPCR/R/MFIaggr.R
chipPCR/R/testxy.R
chipPCR/R/MFIaggr.gui.R
chipPCR/R/inder.R
chipPCR/R/linreg.R
chipPCR/R/effcalc.R
chipPCR/R/AmpSim.R
chipPCR/R/check.method.R
chipPCR/R/fixNA.R
chipPCR/R/th.cyc.R
chipPCR/R/plotCurves.R
chipPCR/vignettes
chipPCR/vignettes/MFIaggr_gui.png
chipPCR/vignettes/humanrater.png
chipPCR/vignettes/datdf.RData
chipPCR/vignettes/roediger-burdukiewicz.bib
chipPCR/vignettes/logo.png
chipPCR/vignettes/logo.pdf
chipPCR/vignettes/natbib.bst
chipPCR/vignettes/browser.png
chipPCR/vignettes/chipPCR.Rnw
chipPCR/vignettes/fixNAevaluation.RData
chipPCR/vignettes/fixNA_test1.png
chipPCR/vignettes/natbib.sty
chipPCR/README.md
chipPCR/MD5
chipPCR/build
chipPCR/build/vignette.rds
chipPCR/DESCRIPTION
chipPCR/man
chipPCR/man/AmpSim.Rd
chipPCR/man/C17.Rd
chipPCR/man/VIMCFX96_60.Rd
chipPCR/man/C67.Rd
chipPCR/man/VIMiQ5_595.Rd
chipPCR/man/C127EGHP.Rd
chipPCR/man/plot-der.Rd
chipPCR/man/Eff1000.Rd
chipPCR/man/C54.Rd
chipPCR/man/bg.max.Rd
chipPCR/man/amptest-class.Rd
chipPCR/man/C317.melt.lr.Rd
chipPCR/man/eff-class.Rd
chipPCR/man/C317.melt.hr.Rd
chipPCR/man/plotCurves.Rd
chipPCR/man/MFIaggr.gui.Rd
chipPCR/man/summary-refMFI.Rd
chipPCR/man/RPA.Rd
chipPCR/man/effcalc.Rd
chipPCR/man/summary-bg.Rd
chipPCR/man/Eff625.Rd
chipPCR/man/plot-refMFI.Rd
chipPCR/man/C60.melt.Rd
chipPCR/man/C316.melt.lr.Rd
chipPCR/man/AmpSim.gui.Rd
chipPCR/man/LAMP.Rd
chipPCR/man/C126EG685.Rd
chipPCR/man/bg-class.Rd
chipPCR/man/capillaryPCR.Rd
chipPCR/man/VIMiQ5_melt.Rd
chipPCR/man/chipPCR.datasets.Rd
chipPCR/man/C81.Rd
chipPCR/man/VIMCFX96_69.Rd
chipPCR/man/plot-bg.Rd
chipPCR/man/C316.amp.Rd
chipPCR/man/CD75.Rd
chipPCR/man/amptester.Rd
chipPCR/man/VIMCFX96_meltcurve.Rd
chipPCR/man/CPP.Rd
chipPCR/man/refMFI-class.Rd
chipPCR/man/th.cyc.Rd
chipPCR/man/th-class.Rd
chipPCR/man/amptester.gui.Rd
chipPCR/man/summary-der.Rd
chipPCR/man/normalizer.Rd
chipPCR/man/smoother.Rd
chipPCR/man/C317.amp.Rd
chipPCR/man/inder.Rd
chipPCR/man/der-class.Rd
chipPCR/man/C126EG595.Rd
chipPCR/man/C85.Rd
chipPCR/man/humanrater.Rd
chipPCR/man/C316.melt.hr.Rd
chipPCR/man/lm.coefs.Rd
chipPCR/man/CD74.Rd
chipPCR/man/chipPCR-package.Rd
chipPCR/man/plot-eff.Rd
chipPCR/man/C60.amp.Rd
chipPCR/man/MFIaggr.Rd
chipPCR/man/VIMiQ5_685.Rd
chipPCR/man/fixNA.Rd
chipPCR/man/Eff750.Rd
chipPCR/man/rounder.Rd
chipPCR/man/Eff875.Rd