Last data update: 2014.03.03
|
aroma.core
Package: aroma.core
Version: 3.0.0
Depends: R (>= 3.1.2), R.utils (>= 2.2.0), R.filesets (>= 2.10.0),
R.devices (>= 2.13.2)
DependsNote: BioC (>= 3.0)
Imports: stats, utils, R.methodsS3 (>= 1.7.0), R.oo (>= 1.19.0),
R.cache (>= 0.12.0), R.rsp (>= 0.21.0), matrixStats (>=
0.50.1), RColorBrewer (>= 1.1-2), PSCBS (>= 0.60.0), listenv,
future
Suggests: png (>= 0.1-7), Cairo (>= 1.5-6), EBImage (>= 4.8.3),
preprocessCore (>= 1.28.0), aroma.light (>= 2.2.1), DNAcopy (>=
1.40.0), GLAD (>= 2.30.0), sfit (>= 0.1.8), expectile (>=
0.2.5), HaarSeg (>= 0.0.2), mpcbs (>= 1.1.1)
SuggestsNote: BioC (>= 3.0), Recommended: aroma.light, DNAcopy, png,
preprocessCore, sfit
Additional_repositories: http://r-forge.r-project.org
Date: 2016-01-05
Title: Core Methods and Classes Used by 'aroma.*' Packages Part of the
Aroma Framework
Authors@R: c(
person("Henrik", "Bengtsson", role=c("aut", "cre", "cph"),
email="henrikb@braju.com"),
person("Mark", "Robinson", role="ctb"),
person("Ken", "Simpson", role="ctb"))
Description: Core methods and classes used by higher-level aroma.* packages
part of the Aroma Project, e.g. aroma.affymetrix and aroma.cn.
License: LGPL (>= 2.1)
URL: https://github.com/HenrikBengtsson/aroma.core,
http://www.aroma-project.org/
BugReports: https://github.com/HenrikBengtsson/aroma.core/issues
LazyLoad: TRUE
biocViews: Microarray, OneChannel, TwoChannel, MultiChannel,
DataImport, DataRepresentation, GUI, Visualization,
Preprocessing, QualityControl, aCGH, CopyNumberVariants
NeedsCompilation: no
Packaged: 2016-01-06 01:12:57 UTC; hb
Author: Henrik Bengtsson [aut, cre, cph],
Mark Robinson [ctb],
Ken Simpson [ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Repository: CRAN
Date/Publication: 2016-01-06 10:01:09
● BiocViews: CopyNumberVariants, DataImport, DataRepresentation, GUI, Microarray, MultiChannel, OneChannel, Preprocessing, QualityControl, TwoChannel, Visualization, aCGH
●
0 images,
132 functions,
0 datasets
●
Reverse Depends: 4
Install log
* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'aroma.core' ...
** package 'aroma.core' successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
Warning in setGenericS3.default(name, export = exportGeneric, envir = envir, :
Renamed the preexisting function apply to apply.default, which was defined in environment base.
Warning in setGenericS3.default(name, export = exportGeneric, envir = envir, :
Renamed the preexisting function write to write.default, which was defined in environment base.
** help
*** installing help indices
converting help for package 'aroma.core'
finding HTML links ... done
AbstractCNData html
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/AbstractCNData.Rd:22: missing file link 'RichDataFrame'
AbstractPSCNData html
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/AbstractPSCNData.Rd:22: missing file link 'RichDataFrame'
AromaCellCpgFile html
AromaCellPositionFile html
AromaCellTabularBinaryFile html
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/AromaCellTabularBinaryFile.Rd:43: missing file link 'AromaCellSequenceFile'
AromaGenomeTextFile html
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/AromaGenomeTextFile.Rd:39: missing file link 'AromaUcscGenomeTextFile'
AromaMicroarrayDataFile html
AromaMicroarrayDataSet html
AromaMicroarrayDataSetTuple html
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/AromaMicroarrayDataSetTuple.Rd:29: missing file link 'AromaUnitTotalCnBinarySetTuple'
AromaMicroarrayTabularBinaryFile html
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/AromaMicroarrayTabularBinaryFile.Rd:41: missing file link 'AromaCellSequenceFile'
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/AromaMicroarrayTabularBinaryFile.Rd:41: missing file link 'AromaUflFile'
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/AromaMicroarrayTabularBinaryFile.Rd:41: missing file link 'AromaUgcFile'
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/AromaMicroarrayTabularBinaryFile.Rd:41: missing file link 'AromaUgpFile'
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/AromaMicroarrayTabularBinaryFile.Rd:41: missing file link 'AromaUnitChromosomeTabularBinaryFile'
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/AromaMicroarrayTabularBinaryFile.Rd:41: missing file link 'AromaUnitGcContentFile'
AromaPlatform html
AromaPlatformInterface html
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/AromaPlatformInterface.Rd:25: missing file link 'AromaCellSequenceFile'
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/AromaPlatformInterface.Rd:25: missing file link 'AromaUflFile'
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/AromaPlatformInterface.Rd:25: missing file link 'AromaUgcFile'
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/AromaPlatformInterface.Rd:25: missing file link 'AromaUgpFile'
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/AromaPlatformInterface.Rd:25: missing file link 'AromaUnitChromosomeTabularBinaryFile'
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/AromaPlatformInterface.Rd:25: missing file link 'AromaUnitGcContentFile'
AromaRepository html
AromaTabularBinaryFile html
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/AromaTabularBinaryFile.Rd:37: missing file link 'AromaCellSequenceFile'
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/AromaTabularBinaryFile.Rd:37: missing file link 'AromaUflFile'
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/AromaTabularBinaryFile.Rd:37: missing file link 'AromaUgcFile'
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/AromaTabularBinaryFile.Rd:37: missing file link 'AromaUgpFile'
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/AromaTabularBinaryFile.Rd:37: missing file link 'AromaUnitChromosomeTabularBinaryFile'
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/AromaTabularBinaryFile.Rd:37: missing file link 'AromaUnitGcContentFile'
AromaTabularBinarySet html
AromaTransform html
AromaUnitCallFile html
AromaUnitCallSet html
AromaUnitFracBCnBinaryFile html
AromaUnitFracBCnBinarySet html
AromaUnitGenotypeCallFile html
AromaUnitGenotypeCallSet html
AromaUnitPscnBinaryFile html
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/AromaUnitPscnBinaryFile.Rd:40: missing file link 'CopyNumberDataFile'
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/AromaUnitPscnBinaryFile.Rd:48: missing file link 'CopyNumberDataFile'
AromaUnitPscnBinarySet html
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/AromaUnitPscnBinarySet.Rd:32: missing file link 'CopyNumberDataSet'
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/AromaUnitPscnBinarySet.Rd:40: missing file link 'CopyNumberDataSet'
AromaUnitSignalBinaryFile html
AromaUnitSignalBinarySet html
AromaUnitTabularBinaryFile html
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/AromaUnitTabularBinaryFile.Rd:45: missing file link 'AromaUflFile'
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/AromaUnitTabularBinaryFile.Rd:45: missing file link 'AromaUgcFile'
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/AromaUnitTabularBinaryFile.Rd:45: missing file link 'AromaUgpFile'
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/AromaUnitTabularBinaryFile.Rd:45: missing file link 'AromaUnitChromosomeTabularBinaryFile'
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/AromaUnitTabularBinaryFile.Rd:45: missing file link 'AromaUnitGcContentFile'
AromaUnitTotalCnBinaryFile html
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/AromaUnitTotalCnBinaryFile.Rd:40: missing file link 'CopyNumberDataFile'
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/AromaUnitTotalCnBinaryFile.Rd:48: missing file link 'CopyNumberDataFile'
AromaUnitTotalCnBinarySet html
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/AromaUnitTotalCnBinarySet.Rd:32: missing file link 'CopyNumberDataSet'
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/AromaUnitTotalCnBinarySet.Rd:40: missing file link 'CopyNumberDataSet'
AromaUnitTypesFile html
BinnedScatter html
CacheKeyInterface html
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/CacheKeyInterface.Rd:25: missing file link 'AromaCellSequenceFile'
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/CacheKeyInterface.Rd:25: missing file link 'AromaUcscGenomeTextFile'
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/CacheKeyInterface.Rd:25: missing file link 'AromaUflFile'
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/CacheKeyInterface.Rd:25: missing file link 'AromaUgcFile'
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/CacheKeyInterface.Rd:25: missing file link 'AromaUgpFile'
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/CacheKeyInterface.Rd:25: missing file link 'AromaUnitChromosomeTabularBinaryFile'
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/CacheKeyInterface.Rd:25: missing file link 'AromaUnitGcContentFile'
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/CacheKeyInterface.Rd:25: missing file link 'CbsSegmentationDataFile'
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/CacheKeyInterface.Rd:25: missing file link 'SampleAnnotationFile'
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/CacheKeyInterface.Rd:25: missing file link 'SegmentationDataFile'
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/CacheKeyInterface.Rd:25: missing file link 'TextUnitNamesFile'
CbsModel html
ChromosomalModel html
ChromosomeExplorer html
CopyNumberChromosomalModel html
CopyNumberSegmentationModel html
Explorer html
FileCacheKeyInterface html
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/FileCacheKeyInterface.Rd:27: missing file link 'AromaCellSequenceFile'
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/FileCacheKeyInterface.Rd:27: missing file link 'AromaUcscGenomeTextFile'
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/FileCacheKeyInterface.Rd:27: missing file link 'AromaUflFile'
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/FileCacheKeyInterface.Rd:27: missing file link 'AromaUgcFile'
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/FileCacheKeyInterface.Rd:27: missing file link 'AromaUgpFile'
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/FileCacheKeyInterface.Rd:27: missing file link 'AromaUnitChromosomeTabularBinaryFile'
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/FileCacheKeyInterface.Rd:27: missing file link 'AromaUnitGcContentFile'
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/FileCacheKeyInterface.Rd:27: missing file link 'CbsSegmentationDataFile'
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/FileCacheKeyInterface.Rd:27: missing file link 'SampleAnnotationFile'
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/FileCacheKeyInterface.Rd:27: missing file link 'SegmentationDataFile'
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/FileCacheKeyInterface.Rd:27: missing file link 'TextUnitNamesFile'
GladModel html
HaarSegModel html
Non-documented_objects html
NonPairedPSCNData html
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/NonPairedPSCNData.Rd:22: missing file link 'RichDataFrame'
PairedPSCNData html
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/PairedPSCNData.Rd:22: missing file link 'RichDataFrame'
ParametersInterface html
RawAlleleBFractions html
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/RawAlleleBFractions.Rd:22: missing file link 'RichDataFrame'
RawCopyNumberModel html
RawCopyNumbers html
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/RawCopyNumbers.Rd:22: missing file link 'RichDataFrame'
RawGenomicSignals html
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/RawGenomicSignals.Rd:22: missing file link 'RichDataFrame'
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/RawGenomicSignals.Rd:30: missing file link 'RichDataFrame'
RawMirroredAlleleBFractions html
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/RawMirroredAlleleBFractions.Rd:22: missing file link 'RichDataFrame'
RawSequenceReads html
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/RawSequenceReads.Rd:22: missing file link 'RichDataFrame'
SegmentedAlleleBFractions html
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/SegmentedAlleleBFractions.Rd:22: missing file link 'RichDataFrame'
SegmentedCopyNumbers html
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/SegmentedCopyNumbers.Rd:22: missing file link 'RichDataFrame'
SegmentedGenomicSignalsInterface html
UnitAnnotationDataFile html
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/UnitAnnotationDataFile.Rd:25: missing file link 'AromaUflFile'
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/UnitAnnotationDataFile.Rd:25: missing file link 'AromaUgcFile'
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/UnitAnnotationDataFile.Rd:25: missing file link 'AromaUgpFile'
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/UnitAnnotationDataFile.Rd:25: missing file link 'AromaUnitChromosomeTabularBinaryFile'
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/UnitAnnotationDataFile.Rd:25: missing file link 'AromaUnitGcContentFile'
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/UnitAnnotationDataFile.Rd:25: missing file link 'TextUnitNamesFile'
UnitNamesFile html
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/UnitNamesFile.Rd:27: missing file link 'TextUnitNamesFile'
UnitTypesFile html
allocate.AromaTabularBinaryFile html
aroma.core-package html
as.GrayscaleImage.matrix html
colBinnedSmoothing.matrix html
colKernelSmoothing.matrix html
display.Explorer html
doCBS html
downloadChipTypeFile.AromaRepository html
downloadFile.AromaRepository html
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/downloadFile.AromaRepository.Rd:32: missing file link 'downloadFile'
estimateSds.CopyNumberChromosomalModel
html
estimateStandardDeviation.RawGenomicSignals
html
exportAromaUnitPscnBinarySet html
extractRawCopyNumbers.CopyNumberChromosomalModel
html
findAnnotationData html
findAnnotationDataByChipType html
findFilesTodo.AromaTransform html
fit.CopyNumberChromosomalModel html
fit.CopyNumberSegmentationModel html
fitGenotypeCone.matrix html
fitGenotypeConeBySfit.matrix html
fitMultiDimensionalCone.matrix html
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/fitMultiDimensionalCone.matrix.Rd:124: missing file link 'backtransformMultiDimensionalCone.matrix'
getAlias.Explorer html
getAromaPlatform.AromaPlatformInterface
html
getCacheKey.CacheKeyInterface html
getCacheKey.FileCacheKeyInterface html
getChipType.AromaPlatformInterface html
getChipType.ChromosomalModel html
getChromosomes.ChromosomalModel html
getChromosomes.ChromosomeExplorer html
getFullName.AromaTransform html
getInputDataSet.AromaTransform html
getModel.ChromosomeExplorer html
getName.AromaTransform html
getName.Explorer html
getNames.ChromosomalModel html
getNames.Explorer html
getOutputDataSet.AromaTransform html
getParameters.ParametersInterface html
getParametersAsString.ParametersInterface
html
getPath.AromaTransform html
getPath.Explorer html
getPlatform.AromaPlatformInterface html
getRootPath.AromaTransform html
getRootPath.Explorer html
getTags.AromaTransform html
getTags.Explorer html
getUnitAnnotationDataFile.AromaPlatformInterface
html
indexOf.UnitNamesFile html
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/indexOf.UnitNamesFile.Rd:39: missing file link 'getUnitNames.UnitNamesFile'
isCompatibleWith.AromaPlatformInterface
html
isDone.AromaTransform html
listFiles.AromaRepository html
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/listFiles.AromaRepository.Rd:28: missing file link 'downloadFile'
matrixBlockPolish.matrix html
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/matrixBlockPolish.matrix.Rd:87: missing file link 'medianPolish.matrix'
mergeBoxplotStats.list html
nbrOfArrays.ChromosomalModel html
nbrOfArrays.Explorer html
nbrOfChipTypes.AromaMicroarrayDataSetTuple
html
Rd warning: /tmp/RtmpwvnVfU/R.INSTALL1e0b506d473b/aroma.core/man/nbrOfChipTypes.AromaMicroarrayDataSetTuple.Rd:35: missing file link 'getChipTypes.AromaMicroarrayDataSetTuple'
nbrOfChipTypes.ChromosomalModel html
plotTracks.PairedPSCNData html
process.AromaTransform html
process.ChromosomeExplorer html
process.Explorer html
processTime html
readFooter.AromaTabularBinaryFile html
segmentByCBS.RawGenomicSignals html
segmentByGLAD.RawGenomicSignals html
segmentByHaarSeg.RawGenomicSignals html
segmentByMPCBS.RawGenomicSignals html
setAlias.Explorer html
setArrays.ChromosomeExplorer html
setArrays.Explorer html
updateSetupExplorerFile.ChromosomeExplorer
html
writeDataFrame.AromaUnitSignalBinaryFile
html
finding level-2 HTML links ... done
writeDataFrame.AromaUnitSignalBinarySet
html
writeDataFrame.AromaUnitTabularBinaryFile
html
writeFooter.AromaTabularBinaryFile html
** building package indices
** testing if installed package can be loaded
* DONE (aroma.core)
Making 'packages.html' ... done
|