Toolkit of Helper Functions to Pre-Process Amplification Data

Documentation for package ‘chipPCR’ version 1.0-2

Help Pages

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