aroma.cn

Package: aroma.cn
Version: 1.6.1
Depends: R (>= 3.1.1), R.utils (>= 2.1.0), aroma.core (>= 2.14.0)
Imports: R.methodsS3 (>= 1.7.0), R.oo (>= 1.19.0), R.filesets (>=
2.9.0), R.cache (>= 0.10.0), matrixStats (>= 0.15.0), PSCBS (>=
0.50.0)
Suggests: aroma.light (>= 2.2.1), DNAcopy (>= 1.40.0), GLAD (>= 1.12.0)
SuggestsNote: BioC (>= 3.0), Recommended: aroma.light, DNAcopy
Date: 2015-10-27
Title: Copy-Number Analysis of Large Microarray Data Sets
Authors@R: c(
person("Henrik", "Bengtsson", role=c("aut", "cre", "cph"),
email="henrikb@braju.com"),
person("Pierre", "Neuvial", role="aut"))
Description: Methods for analyzing DNA copy-number data. Specifically,
this package implements the multi-source copy-number normalization (MSCN)
method for normalizing copy-number data obtained on various platforms and
technologies. It also implements the TumorBoost method for normalizing
paired tumor-normal SNP data.
License: LGPL (>= 2.1)
LazyLoad: TRUE
biocViews: ProprietaryPlatforms, aCGH, CopyNumberVariants, SNP,
Microarray, OneChannel, TwoChannel, DataImport,
DataRepresentation, Preprocessing, QualityControl
URL: http://www.aroma-project.org/
https://github.com/HenrikBengtsson/aroma.cn
BugReports: https://github.com/HenrikBengtsson/aroma.cn/issues
NeedsCompilation: no
Packaged: 2015-10-27 19:42:18 UTC; hb
Author: Henrik Bengtsson [aut, cre, cph],
Pierre Neuvial [aut]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Repository: CRAN
Date/Publication: 2015-10-28 00:08:16

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'aroma.cn' ...
** package 'aroma.cn' successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'aroma.cn'
    finding HTML links ... done
    AbstractCurveNormalization              html  
    MultiSourceCopyNumberNormalization      html  
Rd warning: /tmp/RtmpRI84fK/R.INSTALL5f514f7afe7b/aroma.cn/man/MultiSourceCopyNumberNormalization.Rd:48: missing file link 'AromaUgpFile'
    Non-documented_objects                  html  
    PairedPscbsModel                        html  
Rd warning: /tmp/RtmpRI84fK/R.INSTALL5f514f7afe7b/aroma.cn/man/PairedPscbsModel.Rd:51: missing file link 'dropSegmentationOutliers'
    PrincipalCurveNormalization             html  
    TotalCnBinnedSmoothing                  html  
    TotalCnKernelSmoothing                  html  
    TotalCnSmoothing                        html  
Rd warning: /tmp/RtmpRI84fK/R.INSTALL5f514f7afe7b/aroma.cn/man/TotalCnSmoothing.Rd:46: missing file link 'AromaUgpFile'
    TumorBoostNormalization                 html  
    XYCurveNormalization                    html  
    aroma.cn-package                        html  
    callAllelicBalanceByBAFs.PairedPSCBS    html  
    callCopyNeutralRegions.PairedPSCBS      html  
    callPeaks.PeaksAndValleys               html  
    callXXorXY.numeric                      html  
    cnr                                     html  
Rd warning: /tmp/RtmpRI84fK/R.INSTALL5f514f7afe7b/aroma.cn/man/cnr.Rd:33: missing file link 'CopyNumberRegions'
Rd warning: /tmp/RtmpRI84fK/R.INSTALL5f514f7afe7b/aroma.cn/man/cnr.Rd:37: missing file link 'CopyNumberRegions'
    extractTupleOfDataFiles.MultiSourceCopyNumberNormalization
                                            html  
    findAtomicAberrations.CopyNumberRegions
                                            html  
    fitOne.MultiSourceCopyNumberNormalization
                                            html  
    getAllNames.MultiSourceCopyNumberNormalization
                                            html  
    getFitAromaUgpFile.MultiSourceCopyNumberNormalization
                                            html  
Rd warning: /tmp/RtmpRI84fK/R.INSTALL5f514f7afe7b/aroma.cn/man/getFitAromaUgpFile.MultiSourceCopyNumberNormalization.Rd:29: missing file link 'AromaUgpFile'
    getInputDataSets.MultiSourceCopyNumberNormalization
                                            html  
    getSmoothedDataSets.MultiSourceCopyNumberNormalization
                                            html  
    getSubsetToFit.MultiSourceCopyNumberNormalization
                                            html  
    normalizeBAFsByRegions.PairedPSCBS      html  
Rd warning: /tmp/RtmpRI84fK/R.INSTALL5f514f7afe7b/aroma.cn/man/normalizeBAFsByRegions.PairedPSCBS.Rd:33: missing file link 'normalizeMirroredBAFsByRegions'
Rd warning: /tmp/RtmpRI84fK/R.INSTALL5f514f7afe7b/aroma.cn/man/normalizeBAFsByRegions.PairedPSCBS.Rd:100: missing file link 'normalizeMirroredBAFsByRegions'
    normalizeMirroredBAFsByRegions.matrix   html  
    normalizePrincipalCurve.matrix          html  
    process.MultiSourceCopyNumberNormalization
                                            html  
    testAllelicBalanceByBAFs                html  
** building package indices
** testing if installed package can be loaded
* DONE (aroma.cn)
Making 'packages.html' ... done