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

## Documentation for package ‘ddCt’ version 1.40.0

- 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