# Toolkit of Helper Functions to Pre-Process Amplification Data

## Documentation for package ‘chipPCR’ version 1.0-2

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

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

chipPCR-package | Toolkit of functions to pre-process amplification data

## -- A --

AmpSim | Amplification curve simulator
AmpSim.gui | Amplification Curve Simulation Graphical User Interface
amptest | Class '"amptest"'
amptest-class | Class '"amptest"'
amptester | Amplification test
amptester.gui | Amplification Test Graphical User Interface

## -- B --

bg | Class '"bg"'
bg-class | Class '"bg"'
bg.max | Simple function to detect and correct the background range
bg.max-method | Simple function to detect and correct the background range
bg.max.data.frame | Simple function to detect and correct the background range
bg.max.matrix | Simple function to detect and correct the background range
bg.max.numeric | Simple function to detect and correct the background range

## -- C --

C126EG595 | qPCR Experiment for the Amplification of HPRT1 Using the Bio-Rad iQ5 thermo cycler
C126EG685 | qPCR Experiment for the Amplification of HPRT1 Using the Roche Light Cycler 1.5
C127EGHP | qPCR Experiment for the Amplification of MLC-2v Using the Roche Light Cycler 1.5
C17 | Helicase Dependent Amplification of HPRT1 at Different Temperatures using the 'VideoScan' Platform 2.0
C316.amp | qPCR Experiment for the Amplification of adk Using the Bio-Rad iQ5 thermo cycler
C316.melt.hr | Melting Curves (resolution: 0.2 degrees Celsius / step) for the Gene adk Using the Bio-Rad iQ5 thermo cycler
C316.melt.lr | Melting Curves (resolution: 0.5 degrees Celsius / step) for the Gene adk Using the Bio-Rad iQ5 thermo cycler
C317.amp | qPCR Experiment for the Amplification of adk Using the Bio-Rad CFX96 thermo cycler
C317.melt.hr | Melting Curves (resolution: 0.1 degrees Celsius / step) for the Gene adk Using the Bio-Rad CFX96 thermo cycler
C317.melt.lr | Melting Curves (resolution: 0.5 degrees Celsius / step) for the Gene adk Using the Bio-Rad CFX96 thermo cycler
C54 | qPCR Experiment for the amplification of MLC-2v using the 'VideoScan' heating/cooling-unit
C60.amp | qPCR Experiment for the Amplification of MLC-2v and Vimentin (as decadic dilutions) Using the Roche Light Cycler 1.5
C60.melt | Melt Curves MLC-2v and Vimentin for the qPCR Experiment C60.amp Using the Roche Light Cycler 1.5
C67 | Helicase Dependent Amplification of HPRT1 with different input DNA quantities using the Bio-Rad iQ5 thermo cycler
C81 | Helicase Dependent Amplification of pCNG1 using the 'VideoScan' Platform
C85 | Helicase Dependent Amplification of Vimentin using the 'VideoScan' Platform
capillaryPCR | capillary convective PCR
CD74 | Quantitative PCR with a hydrolysis probe and DNA binding dye
CD75 | Helicase Dependent Amplification in the 'VideoScan' 'HCU'
chipPCR | Toolkit of functions to pre-process amplification data
chipPCR.datasets | Overview for data sets of the 'chipPCR' package
CPP | Curve Pre-processor
CPP-method | Curve Pre-processor
CPP.data.frame | Curve Pre-processor
CPP.matrix | Curve Pre-processor
CPP.numeric | Curve Pre-processor

## -- D --

der | Class '"der"'
der-class | Class '"der"'

## -- E --

eff | Class '"eff"'
eff-class | Class '"eff"'
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
effcalc-method | Analysis of the amplification efficiency
effcalc.data.frame | Analysis of the amplification efficiency
effcalc.matrix | Analysis of the amplification efficiency
effcalc.numeric | Analysis of the amplification efficiency

## -- F --

fixNA | Impute missing values into a column of amplification data
fixNA-method | Impute missing values into a column of amplification data
fixNA.data.frame | Impute missing values into a column of amplification data
fixNA.matrix | Impute missing values into a column of amplification data
fixNA.numeric | Impute missing values into a column of amplification data

## -- H --

humanrater | humanrater, a graphical interface to rate curves

## -- I --

inder | Interpolate derivatives
inder-method | Interpolate derivatives
inder.data.frame | Interpolate derivatives
inder.matrix | Interpolate derivatives
inder.numeric | Interpolate derivatives

## -- L --

LAMP | real-time loop-mediated isothermal amplification (LAMP) by Tanner et al. (2012)
lm.coefs | Compute linear model coefficients

## -- M --

MFIaggr | Multiple comparison of the cycle dependent variance of the fluorescence
MFIaggr-method | Multiple comparison of the cycle dependent variance of the fluorescence
MFIaggr.data.frame | Multiple comparison of the cycle dependent variance of the fluorescence
MFIaggr.gui | Multiple Comparison of the Cycle Dependent Variance - Graphical User Interface
MFIaggr.matrix | Multiple comparison of the cycle dependent variance of the fluorescence
MFIaggr.numeric | Multiple comparison of the cycle dependent variance of the fluorescence

## -- N --

normalizer | Normalize data

## -- P --

plot-method | Class '"amptest"'
plot-method | Plot 'bg' objects
plot-method | Plot 'der' objects
plot-method | Plot 'eff' objects
plot-method | Plot 'refMFI' objects
plot.amptest | Class '"amptest"'
plot.bg | Plot 'bg' objects
plot.der | Plot 'der' objects
plot.eff | Plot 'eff' objects
plot.refMFI | Plot 'refMFI' objects
plotCurves | Plot Curves in an Orthogonal Matrix

## -- Q --

qqline-method | Class '"refMFI"'
qqnorm-method | Class '"refMFI"'

## -- R --

refMFI | Class '"refMFI"'
refMFI-class | Class '"refMFI"'
rounder | Round der objects
RPA | Recombinase polymerase amplification (RPA) by Lutz et al.(2009)

## -- S --

show-method | Class '"amptest"'
show-method | Class '"bg"'
show-method | Class '"der"'
show-method | Class '"eff"'
show-method | Class '"refMFI"'
show-method | Class '"th"'
show.amptest | Class '"amptest"'
show.bg | Class '"bg"'
show.der | Class '"der"'
show.eff | Class '"eff"'
show.th | Class '"th"'
smoother | Wrapper for Several Smoothers of Amplification Data
smoother-method | Wrapper for Several Smoothers of Amplification Data
smoother.data.frame | Wrapper for Several Smoothers of Amplification Data
smoother.matrix | Wrapper for Several Smoothers of Amplification Data
smoother.numeric | Wrapper for Several Smoothers of Amplification Data
summary-der | Summary 'der' objects
summary-method | Class '"amptest"'
summary-method | Class '"eff"'
summary-method | Summary 'bg' objects
summary-method | Summary 'der' objects
summary-method | Summary 'refMFI' objects
summary-method | Class '"th"'
summary.amptest | Class '"amptest"'
summary.bg | Summary 'bg' objects
summary.der | Summary 'der' objects
summary.eff | Class '"eff"'
summary.refMFI | Summary 'refMFI' objects
summary.th | Class '"th"'

## -- T --

th | Class '"th"'
th-class | Class '"th"'
th.cyc | Threshold Cycle

## -- V --

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