Package 'ddCt' reference manual

Title:	The ddCt Algorithm for the Analysis of Quantitative Real-Time PCR (qRT-PCR)
Description:	The Delta-Delta-Ct (ddCt) Algorithm is an approximation method to determine relative gene expression with quantitative real-time PCR (qRT-PCR) experiments. Compared to other approaches, it requires no standard curve for each primer-target pair, therefore reducing the working load and yet returning accurate enough results as long as the assumptions of the amplification efficiency hold. The ddCt package implements a pipeline to collect, analyse and visualize qRT-PCR results, for example those from TaqMan SDM software, mainly using the ddCt method. The pipeline can be either invoked by a script in command-line or through the API consisting of S4-Classes, methods and functions.
Authors:	Jitao David Zhang, Rudolf Biczok, and Markus Ruschhaupt
Maintainer:	Jitao David Zhang <[email protected]>
License:	LGPL-3
Version:	1.61.0
Built:	2024-07-03 05:02:15 UTC
Source:	https://github.com/bioc/ddCt

Barplot with error bars.

Description

Barplot with error bars.

Usage

barploterrbar(y, yl, yh, barcol="orange", errcol="black", horiz=FALSE,
w=0.2,theCut=NULL,columnForDiffBars=TRUE,cex.axis =
par("cex.axis"),zeroForNA=TRUE,legend=FALSE,groups = NULL, order=FALSE, ...)
barploterrbar(y, yl, yh, barcol="orange", errcol="black", horiz=FALSE,
w=0.2,theCut=NULL,columnForDiffBars=TRUE,cex.axis =
par("cex.axis"),zeroForNA=TRUE,legend=FALSE,groups = NULL, order=FALSE, ...)

Arguments

`y`	Numeric vector.
`yl`	Numeric vector of same length as y.
`yh`	Numeric vector of same length as y.
`barcol`	Color of the bars.
`errcol`	Color of the error bars.
`horiz`	Logical. As in `barplot`.
`w`	Size of the error bar ticks.
`theCut`	The cut value
`columnForDiffBars`	Whether the matrix should be transposed (by default the rows are for diff bars)
`zeroForNA`	Draw 0 instead of NA
`cex.axis`	Axis font cex
`legend`	Sould a legend be plotted ?
`groups`	a factor - if specified the bars are collored according to the group they belong to
`order`	plot sample values in descending order
`...`	Further arguments that get passed on to `barplot`.

Details

The function calls barplot with y and decorates it with error bars according to yl and yh.

Value

The function is called for its side effect, producing a plot.

Author(s)

Markus Ruschhaupt, Florian Hahne

Examples

  y <- matrix(runif(80), ncol=5)
  ym <- apply(y, 2, mean)
  dy <- apply(y, 2, sd)*2/sqrt(nrow(y))
  barploterrbar(ym, ym-dy, ym+dy, barcol="#0000c0", errcol="orange")
y <- matrix(runif(80), ncol=5)
  ym <- apply(y, 2, mean)
  dy <- apply(y, 2, sd)*2/sqrt(nrow(y))
  barploterrbar(ym, ym-dy, ym+dy, barcol="#0000c0", errcol="orange")

absolute quantification for Taqman data

Description

absolute quantification for Taqman data

Usage

ddCtAbsolute(raw.table, addData, type = "mean", ADD = -30.234, DIV = -1.6268, sampleInformation = NULL, toZero = FALSE, filename = "warning.output.txt")
ddCtAbsolute(raw.table, addData, type = "mean", ADD = -30.234, DIV = -1.6268, sampleInformation = NULL, toZero = FALSE, filename = "warning.output.txt")

Arguments

`raw.table`	data frame. It must contain columns with the following names:'Ct','Sample','Detector','Platename'. The column 'Ct' must contain numeric values.
`addData`	add data
`type`	character of length 1. 'mean' or 'median'- which method should be used for the aggregation of the repicates
`ADD`	Add constant
`DIV`	Div constant
`sampleInformation`	if specified it must be an object of class `phenoData` with a column named 'Sample'.
`toZero`	boolean - if there is only one replication should the error be treated as zero ? (only if 'type' is mean)
`filename`	character of length 1. The name of the file the warnings should be stored in.

Value

A an object of class eSet. The assayData has the following components: exprs, error, Ct, Ct.error, Difference, number\_NA, number, Plate.

Author(s)

Markus Ruschhaupt mailto:[email protected]

References

~put references to the literature/web site here ~

ddCt Expression

Description

This class is a subclass of ExpressionSet and represents objects which are produced by the ddCt algorithm in the ddCtExpression method

Extends

Class ExpressionSet, directly. Class eSet, by class "ExpressionSet", distance 2. Class VersionedBiobase, by class "ExpressionSet", distance 3. Class Versioned, by class "ExpressionSet", distance 4.

Methods

Ct: signature(object = "ddCtExpression"): returns the Ct value of this ddCtExpressionobject
CtErr: signature(object = "ddCtExpression"): returns the error number of the Ct value of this ddCtExpressionobject
dCt: signature(object = "ddCtExpression"): returns the dCt value of this ddCtExpressionobject
dCtErr: signature(object = "ddCtExpression"): returns the error number of the dCt value of this ddCtExpressionobject
ddCt: signature(object = "ddCtExpression"):returns the ddCt value of this ddCtExpressionobject
ddCtErr: signature(object = "ddCtExpression"): returns the error number of the ddCt value of this ddCtExpressionobject
level: signature(object = "ddCtExpression"): returns the levels in this ddCtExpressionobject
levelErr: signature(object = "ddCtExpression"): returns the error number of the levens in this ddCtExpressionobject
numberCt: signature(object = "ddCtExpression"): returns the Ct number of this ddCtExpressionobject
numberNA: signature(object = "ddCtExpression"): returns the NA number of this ddCtExpressionobject
elist: signature(object = "ddCtExpression"): returns a data frame which represents this expression object
elistWrite: signature(object = "ddCtExpression", file = "character"): writes ddCtExpression object into a file

Author(s)

Rudolf Biczok mailto:[email protected]

Examples

## read a SDM file
sampdat <- SDMFrame(system.file("extdata", "Experiment1.txt",
                                package="ddCt"))

## call ddCtExpression method to get a ddCt calculated expression
result <- ddCtExpression(sampdat,
                         calibrationSample="Sample1",
                         housekeepingGenes=c("Gene1","Gene2"))

## use getter methods
ddCt(result)
ddCtErr(result)
## read a SDM file
sampdat <- SDMFrame(system.file("extdata", "Experiment1.txt",
                                package="ddCt"))

## call ddCtExpression method to get a ddCt calculated expression
result <- ddCtExpression(sampdat,
                         calibrationSample="Sample1",
                         housekeepingGenes=c("Gene1","Gene2"))

## use getter methods
ddCt(result)
ddCtErr(result)

Apply the ddCt algorithm for a given data set

Description

Apply the ddCt algorithm for a given data set

Arguments

`object`	SDMFrame Data object which holds a data set containing columns with the following names: 'Ct','Sample','Detector','Platename'. The column 'Ct' must contain numeric values.
`algorithm`	character. Name of the calibration samples.
`warningStream`	character of length 1. The name of the file the warnings should be stored in.
`calibrationSample`	character. Name of the calibration samples.
`housekeepingGenes`	character. Name of the housekeeping genes.
`type`	character of length 1. 'mean' or 'median'- which method should be used for the aggregation of the repicates
`sampleInformation`	if specified it must be an object of class `phenoData` with a column named 'Sample'.
`toZero`	boolean - if there is only one replication should the error be treated as zero ? (only if 'type' is mean)
`efficiencies`	n.V.
`efficiencies.error`	n.V.

Value

A an object of class ddCtExpression.

usage

ddCtExpression(object, warningStream = "warning.output.txt", algorithm="ddCt" calibrationSample, housekeepingGenes, type="mean", sampleInformation=NULL, toZero=TRUE, efficiencies = NULL, efficiencies.error = NULL)

Methods

object = "InputFrame": An object of InputFrame, constructed with the method InputFrame

Author(s)

Rudolf Biczok mailto:[email protected]

References

Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta -Delta C(T)) Method. KJ Livak and TD Schmittgen, Methods, Vol. 25, No. 4. (December 2001), pp. 402-408

Examples

## read a SDM file
sampdat <- SDMFrame(system.file("extdata", "Experiment1.txt", package="ddCt"))

## call ddCtExpression method from class SDMFrame
## to get a ddCt calculated expression
result <- ddCtExpression(sampdat,
                         calibrationSample="Sample1",
                         housekeepingGenes=c("Gene1","Gene2"))
result
## read a SDM file
sampdat <- SDMFrame(system.file("extdata", "Experiment1.txt", package="ddCt"))

## call ddCtExpression method from class SDMFrame
## to get a ddCt calculated expression
result <- ddCtExpression(sampdat,
                         calibrationSample="Sample1",
                         housekeepingGenes=c("Gene1","Gene2"))
result

Write ddCtExpression object into data frame or files

Description

ddCtExpression object contains a list of matrices as the results of ddCt method. elist combines these lists into one data frame, and elistWrite writes the data frame into file.

summary is a wrapper for the elist method

Usage

elist(object,...)
summary(object,...)
elistWrite(object,file,...)
elist(object,...)
summary(object,...)
elistWrite(object,file,...)

Arguments

`object`	an `ExpressionSet` object.
`file`	output file.
`...`	additional arguments passed to write.table.

Details

elist is a wrapper to as(object, "data.frame") function.

Value

A data frame or output file.

Author(s)

Jitao David Zhang [email protected]

Examples

## read a SDM file
sampdat <- SDMFrame(system.file("extdata", "Experiment1.txt", package="ddCt"))

## call ddCtExpression method from class SDMFrame
## to get a ddCt calculated expression
result <- ddCtExpression(sampdat,
                         calibrationSample="Sample1",
                         housekeepingGenes=c("Gene1","Gene2"))

## call elist
elistResult <- elist(result)
elistResult
## read a SDM file
sampdat <- SDMFrame(system.file("extdata", "Experiment1.txt", package="ddCt"))

## call ddCtExpression method from class SDMFrame
## to get a ddCt calculated expression
result <- ddCtExpression(sampdat,
                         calibrationSample="Sample1",
                         housekeepingGenes=c("Gene1","Gene2"))

## call elist
elistResult <- elist(result)
elistResult

Draw barchart of relative expression level with error-bars

Description

Draw barchart (with error-bars) of relative expression level represented in ddCtExpression object. The barchart is implemented as grid plot by lattice package, where each panel represents one sample and the relative expression values of detectors (as well as their standard errors) are depicted as bars.

Detectors which are not determined are marked by grey ND.

Two types of figures are supported: either condition on samples (by="Sample") or on detectors (by="Detector").

Methods

object = "ddCtExpression", by="character": An object of ddCtExpression, constructed with the method ddCtExpression

Class "errBarchartParameter"

Description

Parameter object for errBarchart

Objects from the Class

Objects can be created by calls of the form new("errBarchartParameter", ...). So far the object is only internally used, but in the near future it will be exported.

Slots

exprsUndeterminedLabel:: Object of class "character", specifying the text label when the expression level is ‘Undetermined’

Methods

exprsUndeterminedLabel: signature(object = "errBarchartParameter"): getting the text label when the expression level is ‘Undetermined’
show: signature(object = "errBarchartParameter"): print method

Note

So far it is only internallly used

Author(s)

Jitao David Zhang <[email protected]>

Examples

## Internally used
## param <- new("errBarchartParameter")
## exprsUndeterminedLabel(param)
## Internally used
## param <- new("errBarchartParameter")
## exprsUndeterminedLabel(param)

Auxillary functions for the executive scripts

Description

getDir creates a directory in case it does not exist and returns the directory name.

Usage

getDir(dir, ...)getDir(dir, ...)

Arguments

`dir`	Directory name
`...`	Other parameters passed to `dir.create`

Details

Auxillary functions

Value

getDir returns the directory name

Author(s)

Jitao David Zhang <[email protected]>

Examples

getDir(tempdir())
getDir(tempdir())

Build an InputFrame from a ReaderClass or a data frame

Description

Generally an InputFrame is built from a ReaderClass (e.g. InputReader), or a data.frame. See the example below for building an object from a valid data.frame.

Usage

  InputFrame(object)
InputFrame(object)

Arguments

object

A data.frame with three columns: Sample, Detector, and Ct

Value

A object of class InputFrame

Author(s)

Jitao David Zhang mailto: [email protected]

Examples

testDf <- data.frame(Sample=rep(paste("Sample", 1:3), each=2),
Detector=rep(paste("Gene", 1:2), 3),
Ct=30+rnorm(6))
testInputFrame <- InputFrame(testDf)
testDf <- data.frame(Sample=rep(paste("Sample", 1:3), each=2),
Detector=rep(paste("Gene", 1:2), 3),
Ct=30+rnorm(6))
testInputFrame <- InputFrame(testDf)

Working with SDM files

Description

The class InputFrame provides core functionalities to read gene and sample information from SDM files and calculate them with a ddCt algorithm.

The function InputFrame reads the data given in the colums 'Detector','Sample' and 'Ct' of the specified SDM output files and stores them as a data.frame. An additional column including the respective filename is added.

Slots

coreData:: Object of class "data.frame": Holds all the required data extracted from the SDM file
files:: Object of class "character" contains the source SDM files

Methods

[,[[,\$: signature(x = "InputFrame"): primitive accessors. Returns an object of InputFrame-class with the subset data.
names: signature(x = "InputFrame"): returns the column names in this SDM object
ddCtExpression: signature(object = "InputFrame"): runs a ddCt algorithm with this SDM object and returns a object of class ddCtExpression
fileNames: signature(object="InputFrame"): returns the source SDM file names.
detectorNames: signature(object = "InputFrame"): returns the detector names in this SDM object
detectorNames<-: signature(object = "InputFrame", value = "character"): replaces the detector names in this SDM object
sampleNames: signature(object = "InputFrame"): returns the sample names in this SDM object
sampleNames<-: signature(object = "InputFrame", value = "character"): replaces the sample names in this SDM object
uniqueDetectorNames: signature(object = "InputFrame"): returns a vector of unique detector names in this SDM object
uniqueDetectorNames<-: signature(object = "InputFrame", target = "missing", value = "character"): replaces all detector names given by the 'names' attribute in 'value' with new detector names
uniqueDetectorNames<-: signature(object = "InputFrame", target = "character", value = "character"): replaces all detector names given by 'target' with new detector names
uniqueSampleNames<-: signature(object = "InputFrame", target = "missing", value = "character"): replaces all sample names given by the 'names' attribute in 'value' with new sample names
uniqueSampleNames<-: signature(object = "InputFrame", target = "character", value = "character"): replaces all sample names given by 'target' with new sample names
uniqueSampleNames: signature(object = "InputFrame"): returns a vector of unique sample names in this SDM object
removeSample: signature(object = "InputFrame", sample="character"): removes the sample(s) specified from the InputFrame object
replaceDetector: signature(object = "InputFrame", target="character", value="character"): replace the detectors equal to the target with the value. Both target and value can be vectors of the same length, then the replace takes place iteratively.
replaceSample: signature(object = "InputFrame", target="character", value="character"): replace the samples equal to the target with the value. Both target and value can be vectors of the same length, then the replace takes place iteratively.
show: signature(object="InputFrame"): pretty print of the InputFrame instance.
rightCensoring: signature(object="InputFrame", threshold="numeric"): Right censoring the Ct value, which targets the data points above a certain value (threshold). High Ct values (higher than 40 or 45 by the rule of thumb) are often not accurate and may indicate too weak expression. The function performs the right censoring on the data and set the value above the threshold as NA (by default) or a given value. See the example.
coreData: signature(object="InputFrame"): returns the data frame read from SDM file.
coreData<-: signature(object="InputFrame"): replace the data frame read from SDM file.
Ct: signature(object="InputFrame"): returns the Ct value of the SDM file.
Ct: signature(object="InputFrame", value="numeric"): replace the Ct value in the object with the new values, and return the object.

Author(s)

Rudolf Biczok mailto:[email protected], Jitao David Zhang mailto:[email protected]

Examples

## read a SDM file
sampdat <- SDMFrame(system.file("extdata", "Experiment1.txt",
                                package="ddCt"))
## you can also write 
## sampdat <- new("SDMFrame",system.file("extdata", "Experiment1.txt",
##                                       package="ddCt"))

## use the getter methods
sampleNames(sampdat)

## or the overloaded primitive accessors
sampdat[1:3,"Sample"]

## see all unique samples
uniqueSampleNames(sampdat)

## replace all sample names 'Sample1' and 'Sample2' in sampdat
## with 'NewSample1' and 'NewSample2'
uniqueSampleNames(sampdat,c("Sample1","Sample2")) <- c("NewSample1","NewSample2")
uniqueSampleNames(sampdat)

## or use this syntax to replace the gene names
uniqueDetectorNames(sampdat) <- c(Gene1="NewGene1", Gene2="NewGene2")
uniqueDetectorNames(sampdat)

## remove sample or detector
removeSample(sampdat, "Sample1")
removeDetector(sampdat, "Gene1")

## replace sample or detector
replaceSample(sampdat, "Sample1", "Sample0")
replaceDetector(sampdat, "Gene1", "PLCG1")

## right censoring the data
rightCensoring(sampdat, 35)
rightCensoring(sampdat, 35, 35)
## read a SDM file
sampdat <- SDMFrame(system.file("extdata", "Experiment1.txt",
                                package="ddCt"))
## you can also write 
## sampdat <- new("SDMFrame",system.file("extdata", "Experiment1.txt",
##                                       package="ddCt"))

## use the getter methods
sampleNames(sampdat)

## or the overloaded primitive accessors
sampdat[1:3,"Sample"]

## see all unique samples
uniqueSampleNames(sampdat)

## replace all sample names 'Sample1' and 'Sample2' in sampdat
## with 'NewSample1' and 'NewSample2'
uniqueSampleNames(sampdat,c("Sample1","Sample2")) <- c("NewSample1","NewSample2")
uniqueSampleNames(sampdat)

## or use this syntax to replace the gene names
uniqueDetectorNames(sampdat) <- c(Gene1="NewGene1", Gene2="NewGene2")
uniqueDetectorNames(sampdat)

## remove sample or detector
removeSample(sampdat, "Sample1")
removeDetector(sampdat, "Gene1")

## replace sample or detector
replaceSample(sampdat, "Sample1", "Sample0")
replaceDetector(sampdat, "Gene1", "PLCG1")

## right censoring the data
rightCensoring(sampdat, 35)
rightCensoring(sampdat, 35, 35)

Class "InputReader"

Description

Abstract factory for data input

Objects from the Class

A virtual Class: No objects may be created from it.

Slots

files:: Input files
colmap:: Column mapping

Author(s)

Rudolf Biczok and Jitao David Zhang

Examples

showClass("InputReader")
showClass("InputReader")

Read QuantStudio file(s)

Description

Read QuantStudio file(s)

Usage

QuantStudioFrame(file)
readQuantStudio(file)
QuantStudioFrame(file)
readQuantStudio(file)

Arguments

file

Character vector of filenames

Details

This function reads the data given in the QuantStudio output files

Value

A object of class SDMFrame

Author(s)

Jitao David Zhang mailto:[email protected]

Examples

sampdat <- QuantStudioFrame(system.file("extdata", c("QuantStudio_File1.txt", "QuantStudio_File2.txt"),package="ddCt"))

## use the getter methods
sampleNames(sampdat)

## or the overloaded primitive accessors
sampdat[1:3,"Sample"]

## see all unique samples
uniqueSampleNames(sampdat)

## replace all sample names 'Sample1' and 'Sample2' in sampdat
## with 'NewSample1' and 'NewSample2'
uniqueSampleNames(sampdat,c("Sample1","Sample2")) <- c("NewSample1","NewSample2")
uniqueSampleNames(sampdat)

## or use this syntax to replace the gene names
uniqueDetectorNames(sampdat) <- c(Hs00559368_m1="Gene1", Hs02576168_g1="Gene2")
uniqueDetectorNames(sampdat)

sampdat <- QuantStudioFrame(system.file("extdata", c("QuantStudio_File1.txt", "QuantStudio_File2.txt"),package="ddCt"))

## use the getter methods
sampleNames(sampdat)

## or the overloaded primitive accessors
sampdat[1:3,"Sample"]

## see all unique samples
uniqueSampleNames(sampdat)

## replace all sample names 'Sample1' and 'Sample2' in sampdat
## with 'NewSample1' and 'NewSample2'
uniqueSampleNames(sampdat,c("Sample1","Sample2")) <- c("NewSample1","NewSample2")
uniqueSampleNames(sampdat)

## or use this syntax to replace the gene names
uniqueDetectorNames(sampdat) <- c(Hs00559368_m1="Gene1", Hs02576168_g1="Gene2")
uniqueDetectorNames(sampdat)

Remove NTC samples

Description

NTC stands for Non-template controls. This method remove the NTC samples from the input object.

Methods

signature(object = "ddCtExpression"): An object hat has been analyzed with the ddCt method
signature(object = "InputFrame"): An input object

REPLACE ITEMS OF VECTOR BY EQUALITY

Description

The function replces (or updates) the items of a given vector by checking the equality with the target parameter. If found, the item will be replaced by the value parameter. The length of both target and value must be the same and could be longer than 1, in which case the replace will be iterated.

Usage

replaceVectorByEquality(vector, target, value)
replaceVectorByEquality(vector, target, value)

Arguments

`vector`	A vector to be replaced. The items of the vector must be atom types, since the equality is checked by '=='.
`target`	targets to be replaced, could be either single or a vector
`value`	values to be replaced at the positions of targets, must be of the same length of `target`

Details

A warning will be prompted if any item in the target cannot be found

Value

A vector of the same length as the parameter vector

Author(s)

Jitao David Zhang

Examples

vector <- c("java", "perl", "python", "c#")
replaceVectorByEquality(vector, target="c#", value="c/c++")
replaceVectorByEquality(vector, target=c("c#","perl"), value=c("c/c++","R"))
vector <- c("java", "perl", "python", "c#")
replaceVectorByEquality(vector, target="c#", value="c/c++")
replaceVectorByEquality(vector, target=c("c#","perl"), value=c("c/c++","R"))

Read an SDM file

Description

Read an SDM file: Data Output File for SDS, Version 2.1

Usage

  SDMFrame(file)
  readSDM(file)
SDMFrame(file)
  readSDM(file)

Arguments

file

Character vector of filenames

Details

This function reads the data given in the colums 'Detector','Sample' and 'Ct' of the specified SDM output file(s) and stores them as a data.frame. An additional column including the respective filename is added.

This function is a wrapper for the SDMFrame constructor

Value

A object of class SDMFrame

Author(s)

Rudolf Biczok mailto:[email protected]

Examples

## read a SDM file
sampdat <- SDMFrame(system.file("extdata", "Experiment1.txt",
                                package="ddCt"))
## you can also write 
## sampdat <- new("SDMFrame",system.file("extdata", "Experiment1.txt",
##                                       package="ddCt"))

## or with
## sampdat <- readSDM(system.file("extdata", "Experiment1.txt",
##                                package="ddCt"))

## use the getter methods
sampleNames(sampdat)

## or the overloaded primitive accessors
sampdat[1:3,"Sample"]

## see all unique samples
uniqueSampleNames(sampdat)

## replace all sample names 'Sample1' and 'Sample2' in sampdat
## with 'NewSample1' and 'NewSample2'
uniqueSampleNames(sampdat,c("Sample1","Sample2")) <- c("NewSample1","NewSample2")
uniqueSampleNames(sampdat)

## or use this syntax to replace the gene names
uniqueDetectorNames(sampdat) <- c(Gene1="NewGene1", Gene2="NewGene2")
uniqueDetectorNames(sampdat)

## read a SDM file
sampdat <- SDMFrame(system.file("extdata", "Experiment1.txt",
                                package="ddCt"))
## you can also write 
## sampdat <- new("SDMFrame",system.file("extdata", "Experiment1.txt",
##                                       package="ddCt"))

## or with
## sampdat <- readSDM(system.file("extdata", "Experiment1.txt",
##                                package="ddCt"))

## use the getter methods
sampleNames(sampdat)

## or the overloaded primitive accessors
sampdat[1:3,"Sample"]

## see all unique samples
uniqueSampleNames(sampdat)

## replace all sample names 'Sample1' and 'Sample2' in sampdat
## with 'NewSample1' and 'NewSample2'
uniqueSampleNames(sampdat,c("Sample1","Sample2")) <- c("NewSample1","NewSample2")
uniqueSampleNames(sampdat)

## or use this syntax to replace the gene names
uniqueDetectorNames(sampdat) <- c(Gene1="NewGene1", Gene2="NewGene2")
uniqueDetectorNames(sampdat)

Write a data frame into an html table within a html page

Description

Write a 'data.frame' into an html table within a html page

Usage

write.htmltable(x, file, title = "", sortby = NULL, decreasing = TRUE, open = "wt")
write.htmltable(x, file, title = "", sortby = NULL, decreasing = TRUE, open = "wt")

Arguments

`x`	'data.frame'
`file`	character. File name.
`title`	character. Title of html page
`sortby`	character. Name of column by which to sort the table rows
`decreasing`	logical. Should the sort order be increasing or decreasing?
`open`	character. This argument is passed onto 'file'

Value

The funciton is called for its side effect: writing a file

Author(s)

Wolfgang Huber

Write a data frame into a tab delimited file

Description

Write a 'data.frame' into a tab delimited file (not quoted and no-row-name TSV file)

Usage

writeSimpleTabCsv(x, file, ...)
writeSimpleTabCsv(x, file, ...)

Arguments

`x`	'data.frame'
`file`	character. File name.
`...`	Additional arguments passed onto the function

Value

The function is called for its side effect: writing a file

Author(s)

Wolfgang Huber

Package 'ddCt'

Help Index

Barplot with error bars.

Description

Usage

Arguments

Details

Value

Author(s)

See Also

Examples

absolute quantification for Taqman data

Description

Usage

Arguments

Value

Author(s)

References

ddCt Expression

Description

Extends

Methods

Author(s)

See Also

Examples

Apply the ddCt algorithm for a given data set

Description

Arguments

Value

usage

Methods

Author(s)

References

See Also

Examples

Write ddCtExpression object into data frame or files

Description

Usage

Arguments

Details

Value

Author(s)

Examples

Draw barchart of relative expression level with error-bars

Description

Methods

Class "errBarchartParameter"

Description

Objects from the Class

Slots

Methods

Note

Author(s)

Examples

Auxillary functions for the executive scripts

Description

Usage

Arguments

Details

Value

Author(s)

Examples

Build an InputFrame from a ReaderClass or a data frame

Description

Usage

Arguments

Value

Author(s)

Examples

Working with SDM files

Description

Slots

Methods

Author(s)

See Also

Examples

Class "InputReader"

Description

Objects from the Class

Slots