aroma.cn v1.6.1
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Copy-Number Analysis of Large Microarray Data Sets
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.
Functions in aroma.cn
| Name | Description | |
| aroma.cn-package | Package aroma.cn | |
| callPeaks.PeaksAndValleys | Calls the peaks in peaks-and-valley estimates | |
| findAtomicAberrations.CopyNumberRegions | Finds all possible atomic regions | |
| callCopyNeutralRegions.PairedPSCBS | Calls regions that are copy neutral | |
| TumorBoostNormalization | The TumorBoostNormalization class | |
| TotalCnKernelSmoothing | The TotalCnKernelSmoothing class | |
| PrincipalCurveNormalization | The PrincipalCurveNormalization class | |
| TotalCnBinnedSmoothing | The TotalCnBinnedSmoothing class | |
| XYCurveNormalization | The XYCurveNormalization class | |
| fitOne.MultiSourceCopyNumberNormalization | Fits the multi-source model for one sample | |
| process.MultiSourceCopyNumberNormalization | Normalizes all samples | |
| callAllelicBalanceByBAFs.PairedPSCBS | Calls regions that are in allelic balance | |
| getAllNames.MultiSourceCopyNumberNormalization | Gets the names of all unique samples across all sources | |
| getSubsetToFit.MultiSourceCopyNumberNormalization | Gets subset of (smoothing) units for fitting the model | |
| normalizeBAFsByRegions.PairedPSCBS | Normalizes allele B fractions (BAFs) based on region-based PSCN estimates | |
| normalizePrincipalCurve.matrix | Normalizes data in K dimensions using principal curves | |
| TotalCnSmoothing | The abstract TotalCnSmoothing class | |
| callXXorXY.numeric | Calls XX or XY from ChrX allele B fractions of a normal sample | |
| getSmoothedDataSets.MultiSourceCopyNumberNormalization | Gets the data sets smoothed toward the UGP file | |
| getInputDataSets.MultiSourceCopyNumberNormalization | Gets the list of data sets to be normalized | |
| testAllelicBalanceByBAFs | Tests for allelic balance in a genomic region | |
| normalizeMirroredBAFsByRegions.matrix | Normalizes region-level mirrored allele B fractions (mBAFs) | |
| Non-documented objects | Non-documented objects | |
| PairedPscbsModel | The PairedPscbsModel class | |
| MultiSourceCopyNumberNormalization | The MultiSourceCopyNumberNormalization class | |
| cnr | Simple creation of a CopyNumberRegions object | |
| AbstractCurveNormalization | The AbstractCurveNormalization class | |
| getFitAromaUgpFile.MultiSourceCopyNumberNormalization | Gets the UGP file specifying the common set of loci to normalize at | |
| extractTupleOfDataFiles.MultiSourceCopyNumberNormalization | Gets a list of data files for a particular name across several data sets | |
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Details
| SuggestsNote | BioC (>= 3.0), Recommended: aroma.light, DNAcopy |
| Date | 2015-10-27 |
| 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 |
| Repository | CRAN |
| Date/Publication | 2015-10-28 00:08:16 |
| depends | aroma , aroma.core (>= 2.14.0) , base (>= 3.1.1) , R (>= 3.1.1) , R.utils (>= 2.1.0) |
| suggests | aroma.light (>= 2.2.1) , DNAcopy (>= 1.40.0) , GLAD (>= 1.12.0) |
| imports | matrixStats (>= 0.15.0) , PSCBS (>= 0.50.0) , R.cache (>= 0.10.0) , R.filesets (>= 2.9.0) , R.methodsS3 (>= 1.7.0) , R.oo (>= 1.19.0) |
| Contributors | Henrik Bengtsson, Pierre Neuvial |
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