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

## Documentation for package ‘ddCt’ version 1.20.0

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

## Help Pages

B C D E F G I L N R S U W misc

## -- B --

barploterrbar | Barplot with error bars.

## -- 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
CSVFrame | Class "InputReader"
CSVReader-class | Class "InputReader"
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
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"
exprsUndeterminedLabel-method | Class "errBarchartParameter"

## -- F --

fileNames | Working with SDM files
fileNames-method | Working with SDM files

## -- G --

getDir | Auxillary functions for the executive scripts

## -- I --

InputFrame | Class "InputReader"
InputFrame-class | Working with SDM files
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

## -- R --

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

## -- 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

## -- 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

## -- misc --

$-method | Working with SDM files
[-method | Working with SDM files
[[-method | Working with SDM files