The ddCt Algorithm for the Analysis of Quantitative Real-Time PCR (qRT-PCR)

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Documentation for package ‘ddCt’ version 1.63.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

A B C D E F G I L N P Q R S T U V W X misc

-- A --

assayData

ddCt Expression

-- B --

barchart	ddCt Expression
barploterrbar	Barplot with error bars.
brewer.pal	ddCt Expression
brewer.pal.info	ddCt Expression

-- C --

ColMap	Class "InputReader"
ColMap-class	Working with SDM files
coreData	Working with SDM files
coreData-method	Working with SDM files
coreData<-	Working with SDM files
coreData<--method	Working with SDM files
Ct	ddCt Expression
Ct-method	Working with SDM files
Ct-method	ddCt Expression
Ct<-	Working with SDM files
Ct<--method	Working with SDM files
CtErr	ddCt Expression
CtErr-method	ddCt Expression

-- D --

dCt	ddCt Expression
dCt-method	ddCt Expression
dCtErr	ddCt Expression
dCtErr-method	ddCt Expression
ddCt	ddCt Expression
ddCt-method	ddCt Expression
ddCtAbsolute	absolute quantification for Taqman data
ddCtErr	ddCt Expression
ddCtErr-method	ddCt Expression
ddCtExpression	Apply the ddCt algorithm for a given data set
ddCtExpression-class	ddCt Expression
ddCtExpression-method	Apply the ddCt algorithm for a given data set
ddCtExpression-methods	Apply the ddCt algorithm for a given data set
DEFAULT.CT.COLNAME	Working with SDM files
DEFAULT.FEATURE.COLNAME	Working with SDM files
DEFAULT.SAMPLE.COLNAME	Working with SDM files
detectorNames	Working with SDM files
detectorNames-method	Working with SDM files
detectorNames<-	Working with SDM files
detectorNames<--method	Working with SDM files

-- E --

elist	Write ddCtExpression object into data frame or files
elist-method	ddCt Expression
elistWrite	Write ddCtExpression object into data frame or files
elistWrite-method	ddCt Expression
errBarchart	Draw barchart of relative expression level with error-bars
errBarchart-method	Draw barchart of relative expression level with error-bars
errBarchart-methods	Draw barchart of relative expression level with error-bars
errBarchartParameter-class	Class "errBarchartParameter"
exprs	ddCt Expression
exprsUndeterminedLabel-method	Class "errBarchartParameter"

-- F --

fData	ddCt Expression
featureData	ddCt Expression
featureNames	ddCt Expression
fileNames	Working with SDM files
fileNames-method	Working with SDM files

-- G --

getDir

Auxillary functions for the executive scripts

-- I --

InputFrame	Build an InputFrame from a ReaderClass or a data frame
InputFrame-class	Working with SDM files
InputFrame-method	Build an InputFrame from a ReaderClass or a data frame
InputFrame-method	Read an SDM file
InputReader-class	Class "InputReader"

-- L --

level	ddCt Expression
level-method	ddCt Expression
levelErr	ddCt Expression
levelErr-method	ddCt Expression

-- N --

names-method	Working with SDM files
numberCt	ddCt Expression
numberCt-method	ddCt Expression
numberNA	ddCt Expression
numberNA-method	ddCt Expression

-- P --

panel.abline	ddCt Expression
panel.barchart	ddCt Expression
panel.grid	ddCt Expression
panel.segments	ddCt Expression
panel.text	ddCt Expression
pData	ddCt Expression
phenoData	ddCt Expression

-- Q --

QuantStudioFrame	Read QuantStudio file(s)
QuantStudioReader-class	Class "InputReader"

-- R --

readQuantStudio	Read QuantStudio file(s)
readSDM	Read an SDM file
removeDetector	Working with SDM files
removeDetector-method	Working with SDM files
removeDetector-methods	Working with SDM files
removeNTC	Remove NTC samples
removeNTC-method	Remove NTC samples
removeNTC-methods	Remove NTC samples
removeSample	Working with SDM files
removeSample-method	Working with SDM files
removeSample-methods	Working with SDM files
replaceDetector	Working with SDM files
replaceDetector-method	Working with SDM files
replaceDetector-methods	Working with SDM files
replaceSample	Working with SDM files
replaceSample-method	Working with SDM files
replaceSample-methods	Working with SDM files
replaceVectorByEquality	REPLACE ITEMS OF VECTOR BY EQUALITY
rightCensoring	Working with SDM files
rightCensoring-method	Working with SDM files
rightCensoring-method	Read an SDM file

-- S --

sampleNames	Working with SDM files
sampleNames-method	Working with SDM files
sampleNames<-	Working with SDM files
sampleNames<--method	Working with SDM files
SDMFrame	Read an SDM file
SDMFrame-class	Working with SDM files
SDMReader-class	Class "InputReader"
show-method	Working with SDM files
show-method	Class "errBarchartParameter"
summary	Write ddCtExpression object into data frame or files

-- T --

TSVFrame	Class "InputReader"
TSVReader-class	Class "InputReader"

-- U --

uniqueDetectorNames	Working with SDM files
uniqueDetectorNames-method	Working with SDM files
uniqueDetectorNames<-	Working with SDM files
uniqueDetectorNames<--method	Working with SDM files
uniqueSampleNames	Working with SDM files
uniqueSampleNames-method	Working with SDM files
uniqueSampleNames<-	Working with SDM files
uniqueSampleNames<--method	Working with SDM files

-- V --

varLabels	ddCt Expression
varMetadata	ddCt Expression

-- W --

write.htmltable	Write a data frame into an html table within a html page
writeSimpleTabCsv	Write a data frame into a tab delimited file

-- X --

xtable

ddCt Expression

-- misc --

"fData<-"	ddCt Expression
"featureData<-"	ddCt Expression
"featureNames<-"	ddCt Expression
"pData<-"	ddCt Expression
"phenoData<-"	ddCt Expression
"varMetadata<-"	ddCt Expression
$-method	Working with SDM files
[-method	Working with SDM files
[[-method	Working with SDM files