Package: codelink 1.75.0
Diego Diez
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.
Authors:
codelink_1.75.0.tar.gz
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codelink.pdf |codelink.html✨
codelink/json (API)
NEWS
| # Install 'codelink' in R: |
| install.packages('codelink', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/ddiez/codelink/issues
- codelink.example - Dataset of class 'Codelink'
- codset - Dataset of class 'CodelinkSet'
On BioConductor:codelink-1.75.0(bioc 3.21)codelink-1.74.0(bioc 3.20)
microarrayonechanneldataimportpreprocessing
Last updated 2 months agofrom:d62058588d. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 05 2024 |
| R-4.5-win | NOTE | Dec 05 2024 |
| R-4.5-linux | NOTE | Dec 05 2024 |
| R-4.4-win | NOTE | Dec 05 2024 |
| R-4.4-mac | NOTE | Dec 05 2024 |
| R-4.3-win | NOTE | Dec 05 2024 |
| R-4.3-mac | NOTE | Dec 05 2024 |
Exports:annotationarrayNewaverageProbesbkgdCorrectchipDevicecodCorrectCodelink2CodelinkSetcodNormalizecodPlotcodPreprocesscodUniversecreateWeightscutCVexprsfc2CondfilterSNRgetBkggetFlaggetInfogetIntgetSNRgetWeightimageCodelinklogCodelinkmeanSNRmergeArrayna2falsenormalizeplotCorrelationplotCVplotDensitiesplotMAprobeNamesprobeTypesreadCodelinkreadCodelinkSetreportCodelinkselCVshowsummarysummaryFlagwriteClusterwriteCodelink
Dependencies:annotateAnnotationDbiaskpassBiobaseBiocGenericsBiostringsbitbit64blobcachemclicpp11crayoncurlDBIfastmapgenericsGenomeInfoDbGenomeInfoDbDatagluehttrIRangesjsonliteKEGGRESTlifecyclelimmamemoisemimeopensslpkgconfigplogrpngR6rlangRSQLiteS4VectorsstatmodsysUCSC.utilsvctrsXMLxtableXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Create a new x11 device | arrayNew |
| Determine the size of the array | arraySize |
| Return a matrix of intensity values | as.matrix.Codelink |
| averageProbes | averageProbes averageProbes,CodelinkSet-method |
| Background correction of intensity values. | bkgdCorrect codCorrect codCorrect,CodelinkSet-method |
| Class Codelink | class:Codelink Codelink Codelink-class show,Codelink-method [,Codelink,ANY,ANY-method [,Codelink-method |
| Dataset of class 'Codelink' | codelink.example |
| Class CodelinkSet | class::CodelinkSet Codelink2CodelinkSet CodelinkSet CodelinkSet-class codPreprocess codPreprocess,CodelinkSet-method exprs,CodelinkSet-method getBkg getBkg,CodelinkSet-method getFlag getFlag,CodelinkSet-method getInfo getInfo,CodelinkSet-method getInt getInt,CodelinkSet-method getSNR getSNR,CodelinkSet-method getWeight getWeight,CodelinkSet-method probeNames probeNames,CodelinkSet-method probeNames,CodelinkSetUnique-method probeTypes probeTypes,CodelinkSet-method |
| Class CodelinkSetUnique | class::CodelinkSetUnique CodelinkSetUnique CodelinkSetUnique-class |
| Diagnostic plots for CodelinkSet object. | codPlot codPlot,CodelinkSet-method codPlot,MArrayLM-method |
| Dataset of class 'CodelinkSet' | codset |
| Create weight for Codelink chips | createWeights createWeights,Codelink-method createWeights,CodelinkSet-method |
| Calculate cutoff based in CV. | cutCV |
| Determine decimal type of Codelink files | decDetect |
| Return the dimension of a Codelink object. | dim.Codelink |
| Select probes based on fold change calculation | fc2Cond |
| Image plot of Codelink arrays | imageCodelink |
| Application of logCodelink to Codelink object | logCodelink |
| Merge Codelink Bioarrays Data | mergeArray |
| Set NAs to FALSE | na2false |
| Normalization wrapper for Codelink/CodelinkSet objects. | codNormalize codNormalize,CodelinkSet-method normalize normalize,Codelink-method normalize,CodelinkSet-method |
| Plot correlation scatterplot between two arrays | plotCorrelation |
| Plot of CV | plotCV |
| Plot Densities | plotDensities plotDensities,Codelink-method |
| MA plot | plotMA |
| Print briefly a Codelink object | printHead |
| Read Codelink Bioarrays Data | readCodelink readCodelinkSet |
| Read Header from Codelink Bioarrays Files | readHeader |
| Read Header from XLS exported Codelink Bioarrays Files | readHeaderXLS |
| Write a report of genes selected in HTML | reportCodelink |
| Select based on CV cutoff. | selCV |
| Calculate SNR | SNR |
| Write a Codelink object to file. | writeCodelink writeCodelink,CodelinkSet-method |
