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.

AuthorDiego Diez
Date of publicationNone
MaintainerDiego Diez <diego10ruiz@gmail.com>
LicenseGPL-2
Version1.42.0
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.

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

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

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