chipPCR: Toolkit of Helper Functions to Pre-Process Amplification Data
Version 0.0.8-10

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.

AuthorStefan Roediger [cre, aut], Michal Burdukiewicz [aut], Konstantin A. Blagodatskikh [ctb]
Date of publication2015-04-10 01:10:56
MaintainerStefan Roediger <stefan.roediger@hs-lausitz.de>
LicenseGPL-3
Version0.0.8-10
URL https://github.com/michbur/chipPCR
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("chipPCR")

Getting started

Package overview
README.md

Popular man pages

AmpSim: Amplification curve simulator
amptester: Amplification test
CD74: Quantitative PCR with a hydrolysis probe and DNA binding dye
Eff625: Highly Replicate Number Amplification Curves
inder: Interpolate derivatives
RPA: Recombinase polymerase amplification (RPA) by Lutz et...
smoother: Wrapper for Several Smoothers of Amplification Data
See all...

All man pages Function index File listing

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

Functions

AmpSim Man page Source code
AmpSim.gui Man page Source code
C126EG595 Man page
C126EG685 Man page
C127EGHP Man page
C17 Man page
C316.amp Man page
C316.melt.hr Man page
C316.melt.lr Man page
C317.amp Man page
C317.melt.hr Man page
C317.melt.lr Man page
C54 Man page
C60.amp Man page
C60.melt Man page
C67 Man page
C81 Man page
C85 Man page
CD74 Man page
CD75 Man page
CPP Man page Source code
CPP,data.frame,missing-method Man page
CPP,matrix,missing-method Man page
CPP,numeric,numeric-method Man page
CPP.data.frame Man page
CPP.matrix Man page
CPP.numeric Man page
Eff1000 Man page
Eff625 Man page
Eff750 Man page
Eff875 Man page
LAMP Man page
MFIaggr Man page Source code
MFIaggr,data.frame,missing-method Man page
MFIaggr,matrix,missing-method Man page
MFIaggr,numeric,numeric-method Man page
MFIaggr.data.frame Man page
MFIaggr.gui Man page Source code
MFIaggr.matrix Man page
MFIaggr.numeric Man page
RGt Source code
RPA Man page
VIMCFX96_60 Man page
VIMCFX96_69 Man page
VIMCFX96_meltcurve Man page
VIMiQ5_595 Man page
VIMiQ5_685 Man page
VIMiQ5_melt Man page
amptest Man page
amptest-class Man page
amptester Man page Source code
amptester.gui Man page Source code
bg Man page
bg-class Man page
bg.max Man page Source code
bg.max,data.frame,missing-method Man page
bg.max,matrix,missing-method Man page
bg.max,numeric,numeric-method Man page
bg.max.data.frame Man page
bg.max.matrix Man page
bg.max.numeric Man page
capillaryPCR Man page
check.method Source code
chipPCR Man page
chipPCR-package Man page
chipPCR.datasets Man page
der Man page
der-class Man page
eff Man page
eff-class Man page
effcalc Man page Source code
effcalc,data.frame,missing-method Man page
effcalc,matrix,missing-method Man page
effcalc,numeric,numeric-method Man page
effcalc.data.frame Man page
effcalc.matrix Man page
effcalc.numeric Man page
first.beginpoint0 Source code
first.beginpoint1 Source code
first.endpoint0 Source code
first.endpoint1 Source code
first.midpoint Source code
fixNA Man page Source code
fixNA,data.frame,missing-method Man page
fixNA,matrix,missing-method Man page
fixNA,numeric,numeric-method Man page
fixNA.data.frame Man page
fixNA.matrix Man page
fixNA.numeric Man page
humanrater Man page Source code
inder Man page Source code
inder,data.frame,missing-method Man page
inder,matrix,missing-method Man page
inder,numeric,numeric-method Man page
inder.data.frame Man page
inder.matrix Man page
inder.numeric Man page
lm.coefs Man page Source code
normalizer Man page Source code
plot,amptest,ANY-method Man page
plot,amptest-method Man page
plot,bg,ANY-method Man page
plot,bg-method Man page
plot,der,ANY-method Man page
plot,der-method Man page
plot,eff,ANY-method Man page
plot,eff-method Man page
plot,refMFI,ANY-method Man page
plot,refMFI,refMFI-method Man page
plot,refMFI-method Man page
plot.amptest Man page
plot.bg Man page
plot.der Man page
plot.eff Man page
plot.refMFI Man page
plotCurves Man page Source code
qqline,refMFI-method Man page
qqnorm,refMFI-method Man page
refMFI Man page
refMFI-class Man page
rounder Man page Source code
rtg.test Source code
sec.beginpoint0 Source code
sec.beginpoint1 Source code
sec.endpoint0 Source code
sec.endpoint1 Source code
sec.midpoint Source code
show,amptest-method Man page
show,bg-method Man page
show,der-method Man page
show,eff-method Man page
show,refMFI-method Man page Man page
show,th-method Man page
show.amptest Man page
show.bg Man page
show.der Man page
show.eff Man page
show.th Man page
smoother Man page Source code
smoother,data.frame,missing-method Man page
smoother,matrix,missing-method Man page
smoother,numeric,numeric-method Man page
smoother.data.frame Man page
smoother.matrix Man page
smoother.numeric Man page
summary,amptest-method Man page
summary,bg-method Man page
summary,der-method Man page
summary,eff-method Man page
summary,refMFI-method Man page
summary,th-method Man page
summary-der Man page
summary.amptest Man page
summary.bg Man page
summary.der Man page
summary.eff Man page
summary.refMFI Man page
summary.th Man page
testxy Source code
th Man page
th-class Man page
th.cyc Man page Source code
th.est Source code

Files

inst
inst/AmpSim.gui
inst/AmpSim.gui/ui.R
inst/AmpSim.gui/server.R
inst/AmpSim.gui/readme.md
inst/AmpSim.gui/DESCRIPTION
inst/CITATION
inst/amptester.gui
inst/amptester.gui/ui.R
inst/amptester.gui/server.R
inst/amptester.gui/amptester_report.Rmd
inst/amptester.gui/DESCRIPTION
inst/MFIaggr.gui
inst/MFIaggr.gui/ui.R
inst/MFIaggr.gui/server.R
inst/MFIaggr.gui/readme.md
inst/MFIaggr.gui/refMFI_report.Rmd
inst/MFIaggr.gui/DESCRIPTION
inst/doc
inst/doc/chipPCR.pdf
inst/doc/chipPCR.Rnw
inst/doc/chipPCR.R
NAMESPACE
CHANGELOG
data
data/VIMiQ5_685.rda
data/C126EG685.rda
data/C81.rda
data/VIMCFX96_60.rda
data/C316.melt.hr.rda
data/C126EG595.rda
data/Eff1000.rda
data/CD74.rda
data/C127EGHP.rda
data/RPA.rda
data/C317.melt.lr.rda
data/C67.rda
data/C60.amp.rda
data/C316.amp.rda
data/C316.melt.lr.rda
data/VIMCFX96_69.rda
data/C60.melt.rda
data/VIMCFX96_meltcurve.rda
data/C85.rda
data/Eff625.rda
data/datalist
data/capillaryPCR.rda
data/VIMiQ5_595.rda
data/C17.rda
data/LAMP.rda
data/Eff750.rda
data/C317.amp.rda
data/CD75.rda
data/C54.rda
data/C317.melt.hr.rda
data/VIMiQ5_melt.rda
data/Eff875.rda
R
R/classes.R
R/smoother.R
R/rounder.R
R/CPP.R
R/amptester.R
R/humanrater.R
R/AmpSim.gui.R
R/lm.coefs.R
R/bg.max.R
R/amptester.gui.R
R/normalizer.R
R/MFIaggr.R
R/testxy.R
R/MFIaggr.gui.R
R/inder.R
R/linreg.R
R/effcalc.R
R/AmpSim.R
R/check.method.R
R/fixNA.R
R/th.cyc.R
R/plotCurves.R
vignettes
vignettes/MFIaggr_gui.png
vignettes/humanrater.png
vignettes/datdf.RData
vignettes/roediger-burdukiewicz.bib
vignettes/logo.png
vignettes/logo.pdf
vignettes/natbib.bst
vignettes/browser.png
vignettes/chipPCR.Rnw
vignettes/fixNAevaluation.RData
vignettes/fixNA_test1.png
vignettes/natbib.sty
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/AmpSim.Rd
man/C17.Rd
man/VIMCFX96_60.Rd
man/C67.Rd
man/VIMiQ5_595.Rd
man/C127EGHP.Rd
man/plot-der.Rd
man/Eff1000.Rd
man/C54.Rd
man/bg.max.Rd
man/amptest-class.Rd
man/C317.melt.lr.Rd
man/eff-class.Rd
man/C317.melt.hr.Rd
man/plotCurves.Rd
man/MFIaggr.gui.Rd
man/summary-refMFI.Rd
man/RPA.Rd
man/effcalc.Rd
man/summary-bg.Rd
man/Eff625.Rd
man/plot-refMFI.Rd
man/C60.melt.Rd
man/C316.melt.lr.Rd
man/AmpSim.gui.Rd
man/LAMP.Rd
man/C126EG685.Rd
man/bg-class.Rd
man/capillaryPCR.Rd
man/VIMiQ5_melt.Rd
man/chipPCR.datasets.Rd
man/C81.Rd
man/VIMCFX96_69.Rd
man/plot-bg.Rd
man/C316.amp.Rd
man/CD75.Rd
man/amptester.Rd
man/VIMCFX96_meltcurve.Rd
man/CPP.Rd
man/refMFI-class.Rd
man/th.cyc.Rd
man/th-class.Rd
man/amptester.gui.Rd
man/summary-der.Rd
man/normalizer.Rd
man/smoother.Rd
man/C317.amp.Rd
man/inder.Rd
man/der-class.Rd
man/C126EG595.Rd
man/C85.Rd
man/humanrater.Rd
man/C316.melt.hr.Rd
man/lm.coefs.Rd
man/CD74.Rd
man/chipPCR-package.Rd
man/plot-eff.Rd
man/C60.amp.Rd
man/MFIaggr.Rd
man/VIMiQ5_685.Rd
man/fixNA.Rd
man/Eff750.Rd
man/rounder.Rd
man/Eff875.Rd
chipPCR documentation built on May 19, 2017, 4:46 p.m.

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

Please suggest features or report bugs in the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.