codelink: Manipulation of Codelink microarray data

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

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("codelink")
AuthorDiego Diez
Bioconductor views DataImport Microarray OneChannel Preprocessing
Date of publicationNone
MaintainerDiego Diez <diego10ruiz@gmail.com>
LicenseGPL-2
Version1.44.0
https://github.com/ddiez/codelink

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.

Functions

annotation,Codelink-method Man page
arrayNew Man page
arraySize Man page
as.matrix.Codelink Man page
averageProbes Man page
averageProbes,CodelinkSet-method Man page
bkgdCorrect Man page
chipDevice Man page
chipDevice,CodelinkSet-method Man page
class:Codelink Man page
class::CodelinkSet Man page
class::CodelinkSetUnique Man page
codCorrect Man page
codCorrect,CodelinkSet-method Man page
Codelink Man page
Codelink2CodelinkSet Man page
Codelink2eSet Man page
[,Codelink,ANY,ANY-method Man page
Codelink-class Man page
codelink.example Man page
[,Codelink-method Man page
CodelinkSet Man page
CodelinkSet-class Man page
CodelinkSetUnique Man page
CodelinkSetUnique-class Man page
codNormalize Man page
codNormalize,CodelinkSet-method Man page
codPlot Man page
codPlot,CodelinkSet-method Man page
codPlot,MArrayLM-method Man page
codPreprocess Man page
codPreprocess,CodelinkSet-method Man page
codset Man page
codUniverse Man page
codUniverse,Codelink-method Man page
codUniverse,CodelinkSet-method Man page
createWeights Man page
createWeights,Codelink-method Man page
createWeights,CodelinkSet-method Man page
cutCV Man page
decDetect Man page
dim.Codelink Man page
eSet2Codelink Man page
exprs,CodelinkSet-method Man page
fc2Cond Man page
filterSNR Man page
filterSNR,Codelink-method Man page
filterSNR,CodelinkSet-method Man page
filterSNR,matrix-method Man page
getBkg Man page
getBkg,CodelinkSet-method Man page
getFlag Man page
getFlag,CodelinkSet-method Man page
getInfo Man page
getInfo,CodelinkSet-method Man page
getInt Man page
getInt,CodelinkSet-method Man page
getSNR Man page
getSNR,CodelinkSet-method Man page
getWeight Man page
getWeight,CodelinkSet-method Man page
guessAnnotation Man page
imageCodelink Man page
logCodelink Man page
meanSNR Man page
meanSNR,CodelinkSet-method Man page
mergeArray Man page
na2false Man page
Nondocumented-objects Man page
normalize Man page
normalize,Codelink-method Man page
normalize,CodelinkSet-method Man page
plotCorrelation Man page
plotCV Man page
plotDensities Man page
plotDensities,Codelink-method Man page
plotMA Man page
printHead Man page
probeNames Man page
probeNames,CodelinkSet-method Man page
probeNames,CodelinkSetUnique-method Man page
probeTypes Man page
probeTypes,CodelinkSet-method Man page
readCodelink Man page
readCodelinkSet Man page
readHeader Man page
readHeaderXLS Man page
reportCodelink Man page
selCV Man page
show,Codelink-method Man page
SNR Man page
summary,Codelink-method Man page
summaryFlag Man page
summaryFlag,Codelink-method Man page
summaryFlag,matrix-method Man page
writeCluster Man page
writeCluster,Codelink-method Man page
writeCluster,CodelinkSet-method Man page
writeCluster,ExpressionSet-method Man page
writeCluster,MArrayLM-method Man page
writeCodelink Man page
writeCodelink,CodelinkSet-method Man page

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.