codelink: Manipulation of Codelink microarray data

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This package facilitates reading, preprocessing and manipulating Codelink microarray data. The raw data must be exported as text file using the Codelink software.

Author
Diego Diez
Date of publication
None
Maintainer
Diego Diez <diego10ruiz@gmail.com>
License
GPL-2
Version
1.42.0
URLs

View on Bioconductor

Man pages

arrayNew
Create a new x11 device
arraySize
Determine the size of the array
as.matrix.Codelink
Return a matrix of intensity values
averageProbes
averageProbes
bkgdCorrect
Background correction of intensity values.
Codelink-class
Class Codelink
codelink.example
Dataset of class 'Codelink'
CodelinkSet-class
Class CodelinkSet
CodelinkSetUnique-class
Class CodelinkSetUnique
codPlot
Diagnostic plots for CodelinkSet object.
codset
Dataset of class 'CodelinkSet'
createWeights
Create weight for Codelink chips
cutCV
Calculate cutoff based in CV.
decDetect
Determine decimal type of Codelink files
dim.Codelink
Return the dimension of a Codelink object.
fc2Cond
Select probes based on fold change calculation
imageCodelink
Image plot of Codelink arrays
logCodelink
Application of logCodelink to Codelink object
mergeArray
Merge Codelink Bioarrays Data
na2false
Set NAs to FALSE
Nondocumented-objects
Here goes every undocumented function.
normalize
Normalization wrapper for Codelink/CodelinkSet objects.
plotCorrelation
Plot correlation scatterplot between two arrays
plotCV
Plot of CV
plotDensities
Plot Densities
plotMA
MA plot
printHead
Print briefly a Codelink object
readCodelink
Read Codelink Bioarrays Data
readHeader
Read Header from Codelink Bioarrays Files
readHeaderXLS
Read Header from XLS exported Codelink Bioarrays Files
reportCodelink
Write a report of genes selected in HTML
selCV
Select based on CV cutoff.
SNR
Calculate SNR
writeCodelink
Write a Codelink object to file.

Files in this package

codelink/DESCRIPTION
codelink/NAMESPACE
codelink/R
codelink/R/Codelink-class.R
codelink/R/CodelinkSet-class.R
codelink/R/CodelinkSet-methods.R
codelink/R/CodelinkSet-tools.R
codelink/R/CodelinkSetUnique-class.R
codelink/R/CodelinkSetUnique-methods.R
codelink/R/cluster.R
codelink/R/data.R
codelink/R/file.R
codelink/R/filter.R
codelink/R/norm.R
codelink/R/plot.R
codelink/build
codelink/build/vignette.rds
codelink/data
codelink/data/codelink.example.rda
codelink/data/codset.rda
codelink/data/datalist
codelink/inst
codelink/inst/CITATION
codelink/inst/NEWS
codelink/inst/doc
codelink/inst/doc/Codelink_Introduction.R
codelink/inst/doc/Codelink_Introduction.Rnw
codelink/inst/doc/Codelink_Introduction.pdf
codelink/inst/doc/Codelink_Legacy.R
codelink/inst/doc/Codelink_Legacy.Rnw
codelink/inst/doc/Codelink_Legacy.pdf
codelink/inst/doc/changelog.txt
codelink/man
codelink/man/Codelink-class.Rd
codelink/man/CodelinkSet-class.Rd
codelink/man/CodelinkSetUnique-class.Rd
codelink/man/Nondocumented-objects.Rd
codelink/man/SNR.Rd
codelink/man/arrayNew.Rd
codelink/man/arraySize.Rd
codelink/man/as.matrix.Codelink.Rd
codelink/man/averageProbes.Rd
codelink/man/bkgdCorrect.Rd
codelink/man/codPlot.Rd
codelink/man/codelink.example.Rd
codelink/man/codset.Rd
codelink/man/createWeights.Rd
codelink/man/cutCV.Rd
codelink/man/decDetect.Rd
codelink/man/dim.Codelink.Rd
codelink/man/fc2Cond.Rd
codelink/man/imageCodelink.Rd
codelink/man/logCodelink.Rd
codelink/man/mergeArray.Rd
codelink/man/na2false.Rd
codelink/man/normalize.Rd
codelink/man/plotCV.Rd
codelink/man/plotCorrelation.Rd
codelink/man/plotDensities.Rd
codelink/man/plotMA.Rd
codelink/man/printHead.Rd
codelink/man/readCodelink.Rd
codelink/man/readHeader.Rd
codelink/man/readHeaderXLS.Rd
codelink/man/reportCodelink.Rd
codelink/man/selCV.Rd
codelink/man/writeCodelink.Rd
codelink/vignettes
codelink/vignettes/Codelink_Introduction.Rnw
codelink/vignettes/Codelink_Legacy.Rnw
codelink/vignettes/codelink.bib