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

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Documentation for package ‘ddCt’ version 1.34.0

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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