Core Methods and Classes Used by 'aroma.*' Packages Part of the Aroma Framework

Core methods and classes used by higher-level aroma.* packages part of the Aroma Project, e.g. aroma.affymetrix and


Package: aroma.core

Version: 3.0.0 [2016-01-05] o SPEED: Segmentation methods (e.g. CbsModel) now uses futures, which means that samples can now be segmented in parallel/distributed. o Package requires R (>= 3.1.2) and BioC (>= 3.0) both released in October 2014. o ROBUSTNESS: Using internally instead of"fcn"). o ROBUSTNESS: Using getPathname() instead of accessing private field. o CLEANUP: Defunct apply() for SampleAnnotationFile; use applyTo(). o CLEANUP: Drop defunct methods. o BUG FIX: getOutputDataSet(..., onMissing="dropall") for AromaTransform would throw error on no applicable method getFullNames() for NULL.

Version: 2.14.0 [2015-10-20] o ROBUSTNESS: Explicitly importing core R functions. o CLEANUP: Renamed apply() for SampleAnnotationFile to applyTo(). o CLEANUP: One rowMads(..., centers) to rowMads(..., center). o CLEANUP: Drop prototype code never used. o CLEANUP: Deprecated internal whatDataType() method. o CLEANUP: Defuncted previously deprecated methods: nbrOfArrays() for readData() for AromaMicroarrayDataSetTuple, AromaMicroarrayDataSet and AromaUnitTotalCnBinarySet, as well as readData() for SampleAnnotationFile. o CLEANUP: Removed previously (Feb 2014) defunct method patchPackage() and patch(). o BUG FIX: writeRegions(..., format="wig") gave an error.

Version: 2.13.1 [2015-05-25] o Package now requires R (>= 3.1.1) released July 2014. This allows us to use BioC (>= 3.0) (October 2014). o Relaxed sanity checks; now it's possible to allocate Aroma tabular binary files with 200e6 rows (was 100e6 rows). o getOutputDataSet() for AromaTransform gives more informative error messages. o ROBUSTNESS: exportAromaUnitPscnBinarySet() asserts that no duplicated files are returned. o ROBUSTNESS: Package now declares all S3 methods. o BUG FIX: getOutputDataSet() for AromaTransform would sometimes given an error due to the same output file being identified more than once, for instance, when the full name of an output file is also the prefix of another file. Thanks to Benilton Carvalho (Universidade Estadual de Campinas, Sao Paulo, Brazil) for reporting on this. o BUG FIX: extractRawMirroredAlleleBFractions() for RawAlleleBFractions gave "Error in setSignals(res, dh) : object 'res' not found".

Version: 2.13.0 [2015-01-07] o Bumped version for CRAN submission. o Updated package dependencies. o Package passes all redundancy tests.

Version: 2.12.8 [2014-09-19] o BUG FIX: display() for Explorer would try to open a pathname in a way that only worked on Windows. Thanks to Sunghee Oh (S. Korea) for reporting on this.

Version: 2.12.7 [2014-09-04] o ROBUSTNESS: Wherever needed, files are now copied without preserving file permissions (e.g. read-only), which became the default in R (>= 2.13.0) [April 2013]. o Bumped package dependencies.

Version: 2.12.6 [2014-08-27] o Now 'aromaSettings' are loaded when the packages is loaded. Previously the package had to be attached. o ROBUSTNESS: Now fit2d() for matrix utilizes use() for aroma.light. o ROBUSTNESS: Added several missing NAMESPACE imports. o BUG FIX: writeDataFrame(..., columnNamesPrefix="none") for AromaUnitSignalBinaryFile would give an error.

Version: 2.12.5 [2014-06-28] o Added getAromaUflFile() for AromaPlatformInterface. o CLEANUP: Move byChipType() from classes AromaCellCpgFile and AromaCellPositionFile to superclass AromaCellTabularBinaryFile. o CLEANUP: Dropped getAromaUgpFile() for AromaUnitSignalBinaryFile. o CLEANUP: Package does less package reordering. o BUG FIX: SampleAnnotationSet$loadAll() would give an error if annotationData/samples/ didn't exist or did not contain any SAF files.

Version: 2.12.4 [2014-06-09] o Package now requires R (>= 3.0.0) and BioC (>= 2.13), which were released April 2013 and are in fact old and it's recommended to use a more recent version of R. o Added 'SuggestsNote' field to DESCRIPTION with list of packages that are recommended for the most common use cases. o Bumped package dependencies.

Version: 2.12.3 [2014-05-02] o CLEANUP: Now using ds[[idx]] instead of getFile(ds, idx) where possible.

Version: 2.12.2 [2014-04-26] o SPEEDUP: Minor speedup by replacing repetive ::() calls with repetive () calls; the '::' operator is fairly expensive.

Version: 2.12.1 [2014-03-04] o CRAN POLICY: Now limiting the number of registered S3 methods in NAMESPACE for R (< 3.1.0). Used to be R (< 3.0.2).

Version: 2.12.0 [2014-03-01] o Bumped version for CRAN submission. o Updated package dependencies. o Package passes all redundancy tests.

Version: 2.11.7 [2014-02-28] o Now methods that supports searching sibling root directories do so by default. Previously this had to be explicitly enabled via an option. o Updated package dependencies. o CLEANUP: Defuncted previously deprecated downloadPackagePatch() and patchPackage() as well as patch() for AromaPackage. o CLEANUP: Removed defunct methods.

Version: 2.11.6 [2014-02-17] o BUG FIX: The GladModel would not pass user-specified arguments. Thanks to Hans-Ulrich Klein at University of M�nster for reporting on this.

Version: 2.11.5 [2014-02-03] o BUG FIX: readDataFrame() for AromaGenomeTextFile and AromaUcscGenomeTextFile explicitly passed arguments '...' to NextMethod(), which would cause them to be duplicated in certain cases.

Version: 2.11.4 [2014-01-17] o CLEANUP: Now all Explorer classes utilize R.rsp::rfile() for compiling RSP files instead of the to-be-deprecated rspToHtml().

Version: 2.11.3 [2014-01-16] o BUG FIX: getGenericSummary() for RichDataFrame would throw "Error in data[i, , drop = FALSE] : subscript out of bounds" if it had zero rows.

Version: 2.11.2 [2013-12-11] o Added findChangePointsByState() for SegmentedGenomicSignalsInterface. o DOCUMENTATION: Added documentation for exportAromaUnitPscnBinarySet().

Version: 2.11.1 [2013-11-15] o Added argument 'onMissing' to getOutputDataSet() for AromaTransform. This replaces argument 'incomplete', which will be dropped in a future version, but is for now supported as well.

Version: 2.11.0 [2013-10-16] o CLEANUP: Minor adjustments of NAMESPACE imports. o CLEANUP: Dropped colMedians() for AromaTabularBinaryFile. If needed, there is always colStats(). o Updated package dependencies. o Now package requires R (>= 2.15.0) [and Bioc (>= 2.10.0)].

Version: 2.10.6 [2013-10-07] o CLEANUP: Now explicitly importing only what is needed in NAMESPACE. o BACKWARD COMPATIBILITY: For R (< 3.0.2) only the maximum of 500 S3 methods are declared in NAMESPACE. o Updated package dependencies.

Version: 2.10.5 [2013-10-03] o Added argument 'chromosomes' to ChromosomalModel() and setChromosomes() for the same class. If not specified, the default is as before to infer the set of chromosomes from the UGP files. o HELP: Now the sanity-check error that CopyNumberChromosomalModel throws gives a more informative error message suggesting to adjust argument 'maxNAFraction' when setting up the model.

Version: 2.10.4 [2013-09-28] o Now the 'aroma.core' Package object is also available when the package is only loaded (but not attached). o CLEANUP: Now only importing the exact set of methods needed from the 'R.utils' package.

Version: 2.10.3 [2013-09-20] o CLEANUP: Now only importing the exact set of methods needed from the 'matrixStats' package. o ROBUSTNESS: Forgot to import R.methodsS3::appendVarArgs(). o Updated package dependencies.

Version: 2.10.2 [2013-09-11] o CLEANUP: Backward-compatibility code for obsolete EBImage was no longer needed. o CLEANUP: Updated package dependencies.

Version: 2.10.1 [2013-08-12] o BUG FIX: exportAromaUnitPscnBinarySet() for AromaUnitTotalCnBinarySet would throw an error on "unknown argument 'names' to indexOf()".

Version: 2.10.0 [2013-08-03] o Bumped version for CRAN submission. o Updated package dependencies. o Package passes all redundancy tests.

Version: 2.9.7 [2013-07-20] o CLEANUP: Replaced all internal x11() with calls. o CLEANUP: Moved more packages from Depends to Imports. o Updated package dependencies.

Version: 2.9.6 [2013-06-01] o Added findFilesTodo() for AromaTransform.

Version: 2.9.5 [2013-05-30] o DOCUMENTATION: Now help("doCBS") documents all doCBS() methods. o Now it's possible to call aroma.core::doCBS() without loading package. o Turned doCBS() into a default method, cf. aroma.affymetrix::doRMA().

Version: 2.9.4 [2013-05-25] o SPEEDUP: Replaced all rm() calls with NULL assignments.

Version: 2.9.3 [2013-05-22] o CLEANUP: Now using getChecksum() instead of (internal) R.filesets::digest2() with identical results.

Version: 2.9.2 [2013-05-22] o BUG FIX: extractRawCopyNumbers() for CopyNumberChromosomalModel would throw 'Error in UseMethod("getChecksum") : no applicable method for 'getChecksum' applied to an object of class "list"' if (and only if) R.cache package was not attached. Thanks Yadav Sapkota at University of Alberta for reporting on this.

Version: 2.9.1 [2013-05-20] o CRAN POLICY: Now all Rd \usage{} lines are at most 90 characters long. o CRAN POLICY: Now all Rd example lines are at most 100 characters long.

Version: 2.9.0 [2013-04-23] o No updates. o Bumped version for CRAN submission. o Package passes all redundancy tests.

Version: 2.8.7 [2013-04-22] o CLEANUP: Package no longer try to apply package patches, which was only possible when namespaces where not used. o CLEANUP: Package no longer depends on R.cache (only imports it).

Version: 2.8.6 [2013-04-21] o CLEANUP: Made is(Homo|Hetero)zygote() and getPhysicalPositions() defunct.

Version: 2.8.5 [2013-04-08] o Updated package dependencies.

Version: 2.8.4 [2013-03-28] o Added the sqrtsign() transform. This makes it possible to plot log2 PLM residuals (in aroma.affymetrix) on a blue-to-red scale using setColorMaps(.., "log2,sqrtsigned,bluewhitered") where bluewhitered <- colorRampPalette(c("blue", "white", "red")).

Version: 2.8.3 [2013-03-23] o Bumped the package dependencies. o Added an Authors@R field to DESCRIPTION.

Version: 2.8.2 [2013-03-05] o DOCUMENTATION: Updated the help usage section for all static methods. o Bumped up package dependencies.

Version: 2.8.1 [2013-01-03] o CLEANUP: Deprecated nbrOfArrays() for AromaMicroarrayDataSet and AromaUnitTotalCnBinarySet. o CLEANUP: Some of the internal aroma.core code still called deprecated methods resulting in unnecessary warnings.

Version: 2.8.0 [2012-12-21] o No updates. o Bumped version for CRAN submission. o Package passes all redundancy tests.

Version: 2.7.6 [2012-12-20] o Bumped up package dependencies. o Now using argument 'colClasses' (was 'colClassPatterns') for all readDataFrame():s. o Utilizing new startupMessage() of R.oo.

Version: 2.7.5 [2012-12-06] o ROBUSTNESS: Utilizing new getOneFile() internally.

Version: 2.7.4 [2012-12-04] o CLEANUP: Dropped inst/reports/templates/html/archive/, inst/reports/templates/rsp/archive/ and inst/archive/, which all contained old/legacy Explorer versions.

Version: 2.7.3 [2012-11-29] o Renamed lapply() for AromaTabularBinaryFile to colApply().

Version: 2.7.2 [2012-11-28] o Made several file classes implement FileCacheKeyInterface. o Added CacheKeyInterface and FileCacheKeyInterface.

Version: 2.7.1 [2012-11-26] o Lowered the package dependencies to aroma.light (>= 1.22.0) such that this package can be installed easily on R (>= 2.14.0). o BUG FIX: getRam() and setRam() for AromaSettings did not use 'memory/ram'.

Version: 2.7.0 [2012-11-24] o Bumped version for CRAN submission. o Bumped up package dependencies. o No updates. o Package passes all redundancy tests.

Version: 2.6.16 [2012-11-21] o Now getParametersAsString() handles sets of parameters as well. o Added getParameterSets() to ParametersInterface.

Version: 2.6.15 [2012-11-21] o Added ParametersInterface. o DOCUMENTATION: Hiding more internal methods from the help indices.

Version: 2.6.14 [2012-11-18] o CLEANUP: Dropped getHeaderParameters() for TextUnitNamesFile, which is now done by getHeader() of TabularTextFile. o CLEANUP: Now using getName() instead of deprecated getLabel(). o CLEANUP: Package only depends on digest indirectly via R.cache. o CLEANUP: Moved internal .assertDigest() to R.cache.

Version: 2.6.13 [2012-11-13] o CLEANUP: Properly declared all cached fields, making it possible to remove nearly all clearCache() implementations because the one for Object takes does the job. o CLEANUP: The RSP template for ChromosomeExplorer's setupExplorer.js had a duplicated entry.

Version: 2.6.12 [2012-11-12] o CLEANUP: Now seq_along(x) instead of seq(along=x) everywhere. Similarly, seq(ds) where 'ds' is GenericDataFileSet is now replaced by seq_along(ds). Likewise, seq_len(x) replaces seq(length=x), and length(ds) replaces nbrOfFiles(ds).

Version: 2.6.11 [2012-11-08] o Renamed getColumnNames() to getDefaultColumnNames() for all classes inheriting from GenericTabularFile, because of the new ColumnNamesInterface interface. o CRAN POLICY: Made a few of the examples faster. Also made some of the system tests faster.

Version: 2.6.10 [2012-11-05] o CLEANUP: Replaced all whichVector() with which(), because the latter is now the fastest again.

Version: 2.6.9 [2012-10-31] o Added argument 'units' to readDataFrame() for AromaUnitChromosomeTabularBinaryFile.

Version: 2.6.8 [2012-10-29] o CLEANUP: Now using Arguments$get(Read|Writ)ablePath() instead of filePath(..., expandLinks="any").

Version: 2.6.7 [2012-10-21] o Added argument 'maxNAFraction' to CopyNumberChromosomalModel, which is now the prefer place to specify it, instead of to fit() etc. o Now CopyNumberChromosomalModel() accepts references of type "none", "constant(1)", "constant(2)", and "median", where "none" and "constant(1)" are identical, "constant(2)" uses reference signals that are exactly 2, and "median" uses reference signals are equals the robust average across all samples. For backward compatibility, NULL is still supported, which equals "median". o ROBUSTNESS: Now using Arguments$getWritablePath() everywhere instead of mkdirs(), because the former will do a better job in creating and asserting directories on slow shared file systems, and when it fails it gives a more informative error message. o BUG FIX: Scrolling in the ChromosomeExplorer by dragging the navigator bar was broken.

Version: 2.6.6 [2012-10-18] o It is no longer possible to have different versions of ArrayExplorer and ChromosomeExplorer under the same reports/ directory structure. If you wish to keep old Explorer reports, rename those reports/ root directories. o ROBUSTNESS/BUG FIX: Some of the HTML and CSS errors in ArrayExplorer and ChromosomeExplorer that were detected by the W3's online validation services were correct. o BUG FIX: A few errors in the Javascript of ArrayExplorer has been corrected. It also does a better job of inferring the height of the displayed spatial image. Thanks Laurent Malvert (ID Business Solutions Ltd; IDBS) for the report, troubleshooting and suggestions on this.

Version: 2.6.5 [2012-10-17] o ROBUSTNESS: Now all static Object methods that calls "next" methods, utilizes NextMethod(), which became possible with R.oo v1.10.0.

Version: 2.6.4 [2012-10-16] o ROBUSTNESS/BUG FIX: No longer passing '...' to NextMethod(), cf. R-devel thread 'Do not pass '...' to NextMethod() - it'll do it for you; missing documentation, a bug or just me?' on Oct 16, 2012.

Version: 2.6.3 [2012-10-14] o Added AromaUnitGcContentFile (from aroma.affymetrix). o CLEANUP: Removed several defunct/obsolete methods and made deprecated methods defunct/obsolete.

Version: 2.6.2 [2012-10-11] o Now aroma.core imports R.methodsS3 and R.oo. This solves issues such as trim() being overridden by ditto from the IRanges package, iff loaded.

Version: 2.6.1 [2012-09-14] o Added exportAromaUnitPscnBinarySet() for a list. o BUG FIX: exportAromaUnitPscnBinarySet() for AromaUnitTotalCnBinarySet would throw an error if the files of the exported data set was ordered in a non-lexicographic order.

Version: 2.6.0 [2012-09-05] o Submitted to CRAN. o The package passes all redundancy tests.

Version: 2.5.14 [2012-09-04] o Added downloadUGC() for AromaRepository.

Version: 2.5.13 [2012-09-02] o BUG FIX: interleave() for Image and RasterImage could generate error 'Error in if (abs(vRatio) > abs(hRatio)) { : missing value where TRUE/FALSE needed' if odd/even cell intensity columns (rows) contained all NAs.

Version: 2.5.12 [2012-08-31] o GENERALIZATION: Now downloadCDF() for AromaRepository downloads CDFs regardless of *.cdf and *.CDF.

Version: 2.5.11 [2012-08-29] o ROBUSTNESS: Added argument 'escape' to findAnnotationData(), which causes such symbols that exist in argument 'pattern' to be automatically be escaped.

Version: 2.5.10 [2012-08-26] o DOCUMENTATION: Clarified that when colBinnedSmoothing() is done over zero-length bins, the output for those bins will be NA. o BUG FIX: colBinnedSmoothing(..., xOut=xOut) would return binned values in the incorrect order, iff 'xOut' was not ordered. Added a systems test for this case. o BUG FIX: colBinnedSmoothing(..., xOut=xOut) could generate bins at the ends that did not contain the outer most 'xOut' values.

Version: 2.5.9 [2012-08-22] o Improved the AromaRepository class.

Version: 2.5.8 [2012-08-21] o ROBUSTNESS: Now the package startup message is outputted at the very end. Previously it was done before some additional setup, which could potentially fail. o ROBUSTNESS: fitWRMA() and fitWHRCModel() now call rcModelWPLM() of preprocessCore instead of .Call(..., PACKAGE="preprocessCore"). Doing so will somewhat slow down the speed, because rcModelWPLM() introduces some non-needed validation of the arguments. This caused their arguments 'psiCode' and 'psiK' to be dropped.

Version: 2.5.7 [2012-08-08] o ROBUSTNESS: Added 'preprocessCore' as a suggested package, because some of the internal functions rely on that package. This was never an issue, because those functions were called by wrapper functions in aroma.affymetrix that assert that the package is indeed loaded.

Version: 2.5.6 [2012-07-21] o Added exportAromaUnitPscnBinarySet() for AromaUnitTotalCnBinarySet. o Added alpha versions of classes AromaUnitPscnBinary(File|Set). o Added getNumberOfFilesAveraged() to AromaUnitSignalBinaryFile. Formerly only for AromaUnitTotalCnBinaryFile.

Version: 2.5.5 [2012-07-17] o Updated package dependencies.

Version: 2.5.4 [2012-07-10] o Now package imports R.devices, because it uses some of its device drivers that previously were in R.utils.

Version: 2.5.3 [2012-06-18] o FIX: Fixed a typo in an error message generated by byChipType() for several annotation data file classes.

Version: 2.5.2 [2012-05-30] o Updated package dependencies. o Added argument 'calculateRatios' to CopyNumberChromosomalModel().

Version: 2.5.1 [2012-04-16] o CLEANUP: Package now only depends/imports on CRAN package, which simplifies the installation of aroma.core, and indirectly any packages that depends on it. Note, there are still "suggested" non-CRAN packages, which are required by some/optional methods. o CLEANUP: Package no longer depends on aroma.light, but instead it "suggests" it. This is possible, because now weightedMad() of aroma.light has been added to matrixStats v0.5.0. o CLEANUP: Package no longer "Suggests" affxparser. It was needed because of the findFiles() function, which has been added to R.utils v1.13.1.

Version: 2.5.0 [2012-03-25] o Submitted to CRAN. o The package passes all redundancy tests.

Version: 2.4.13 [2012-03-23] o Added alpha versions of PairedPSCNData and NonPairedPSCNData, which inherits from RawGenomicSignals. o Turned weightedMad() into a default method, added help documentation with example code. o CLEANUP: Moved (internal) swapXY() and draw() for 'density' objects to R.utils (>= 1.10.0). o BUG FIX: "["() for RichDataFrame would loose the class attribute, unless argument 'drop' was FALSE.

Version: 2.4.12 [2012-03-15] o Now colBinnedSmoothing(), colKernelSmoothing() and colGaussianSmoothing() returns a matrix with column names as in argument 'Y'. o For RawGenomicSignals, added argument 'fields' to binnedSmoothing() and binnedSmoothingByField(). Also added argument 'field' to getSignals() and estimateStandardDeviation(). o Now RawGenomicSignals extends new internal RichDataFrame class. o CLEANUP: Dropped deprecated files from the reports/includes/js/ directory installed by ArrayExplorer and ChromosomeExplorer.

Version: 2.4.11 [2012-03-12] o Added binnedSmoothingByField() for RawGenomicSignals. o Added subset() for RawGenomicSignals. o Added get- and setVirtualField() for RawGenomicSignals. o Added argument 'sort' to for RawGenomicSignals.

Version: 2.4.10 [2012-03-06] o GENERALIZATION: The new ArrayExplorer v3.4 will work with most commonly used web browsers including Mozilla Firefox, Google Chrome, Microsoft Internet Explorer, Apple Safari, and Opera.

Version: 2.4.9 [2012-03-06] o ROBUSTNESS: Now all writeDataFrame() methods will add quotation marks around column names that contain a comment character ('#'). This will make the written file readable with read.table() even when there are header comments with prefix '#'. This issue was reported by Yu Song at Oakland University. o Now createImage() for matrix creates images of type "png::array" by default (used to be "EBImage::Image"). If the latter, then at least EBImage v3.9.7 (July 2011) is required. o BUG FIX: write() for RasterImage would write truncated intensities, because we forgot to rescale [0,65535] to [0,1] intensities.

Version: 2.4.8 [2012-03-02] o GENERALIZATION: Now RawGenomicSignals inherits from data.frame instead of Object. It works with the big aroma.affymetrix test suite as well as with the TCGA vignette (of

Version: 2.4.7 [2012-03-01] o Preparing for RawGenomicSignals not being reference variables. o Preparing for supporting multiple-chromosome RawGenomicSignals. o ROBUSTNESS: Added system tests for RawGenomicSignals classes. o CLEANUP: Now R CMD check no longer reports that the package is using .Internal() function calls. This was due to how we adjusted colSums() and colMeans() to become generic functions.

Version: 2.4.6 [2012-02-04] o Created ChromosomeExplorer v3.4, which should work on even more browsers. o GENERALIZATION: Now binnedSmoothing() of RawGenomicSignals default to generate the same target bins as binnedSmoothing() of a numeric vector. Before the bins had to be specified explicitly by the caller. o GENERALIZATION: Now it is possible to call colBinnedSmoothing() with an empty set of input loci, but still requesting a set of output loci, which then will be all missing values. o BUG FIX: Argument 'x' of colBinnedSmoothing() would default to the incorrect number of loci.

Version: 2.4.5 [2012-02-03] o GENERALIZATION: As ChromosomeExplorer v3.3, the new ArrayExplorer v3.3 works with most common web browsers. See below. However, we still have problems getting ArrayExplorer to load the main spatial (PNG) image in Internet Explorer. o Forgot to include require.js in v2.4.4, which is needed by the ChromosomeExplorer v3.3.

Version: 2.4.4 [2012-02-01] o GENERALIZATION: The new ChromosomeExplorer v3.3 will work with most commonly used web browsers including Mozilla Firefox, Google Chrome, Microsoft Internet Explorer, Apple Safari and Opera. This far it has been tested with the following browsers: Firefox v3.6/v9.01/v10.0, Chrome v17.0, IE v7.x/v9.0, and Safari 5. NOTE: To update an existing ChromosomeExplorer report, call setup(ce, force=TRUE) where 'ce' is your ChromosomeExplorer object. Thanks to Keith Ching at ConsultChing for the initial troubleshooting [] leading me on the right track on how update ChromosomeExplorer.

Version: 2.4.3 [2012-01-17] o ROBUSTNESS: Now findPngDevice() tries all the available settings for argument "type" of png(), for the current platform. This will increase the chances for finding a PNG device that really works. o SPEEDUP: Now findPngDevice() memoizes the results throughout the current session. o CLEANUP: Now findPngDevice() uses isPackageInstalled("Cairo") instead of require("Cairo") to avoid loading Cairo if not really used.

Version: 2.4.2 [2012-01-14] o BUG FIX: drawCytoband() for ChromosomalModel failed to locate the genome annotation data file containing cytoband information, e.g. Human,cytobands,.txt. Thanks to Kai Wang at Pfizer for reporting on this. o Added tag 'hg17' to Human,cytobands,hg17,GLADv2.4.0,HB20100219.txt in annotationData/genomes/Human/.

Version: 2.4.1 [2012-01-12] o CLEANUP: Dropped internal patch of base::serialize(), because it was only applied to R (< 2.12.0) anyway and this package now requires R (>= 2.12.0).

Version: 2.4.0 [2012-01-11] o ROBUSTNESS: Aroma settings are no longer loaded during R CMD check. o Updated package dependencies.

Version: 2.3.7 [2011-12-22] o BUG FIX: The overridden library() would always return an invisible() object, even if base::library() wouldn't. This caused plain library() to not list installed packaged. Thanks Venkat Seshan at MSKCC for reporting on this.

Version: 2.3.6 [2011-12-15] o Now colBinnedSmoothing() handles an unordered 'xOut'. o Added argument 'units' to writeDateFrame() for AromaUnitSignalBinarySet to make it possible to write any subset of units and in any order, e.g. genome order.

Version: 2.3.5 [2011-12-11] o Now it is possible to fully specify the location and the width of each bin used by colBinnedSmoothing(), which now also returns the bin counts as part of the attributes. Moreover, the bins are now defined to be strictly disjoint using boundaries [x0,x1) instead of [x0,x1] as before. o Added plotCoverageMap() for AromaUgpFile.

Version: 2.3.4 [2011-11-19] o Now byChipType() for UnitAnnotationDataFile and derivatives give an error message with more information on which file it failed to locate, e.g. by specifying filename extension it looked for. o Added default getDefaultExtension() for UnitAnnotationDataFile, which guesses the filename extension from the class name, unless overridden by a subclass. o CLEANUP: Now getFullNames() for AromaMicroarrayDataSetTuple no longer produces a warning on " applied to non-(list or vector) of type 'NULL'". o BUG FIX: exportTotalCnRatioSet() for AromaUnitTotalCnBinarySet and exportFracBDiffSet() for AromaUnitTotalCnBinarySet tried to call cat(verbose, x) with length(x) > 1.

Version: 2.3.3 [2011-11-17] o Added trial version of AromaUcscGenomeTextFile.

Version: 2.3.2 [2011-11-14] o BUG FIX: process() of ChromosomeExplorer would throw "Error in file(file, ifelse(append, "a", "w")) : [...] cannot open file '/ [...] (new Array(': No such file or directory". Importing the R.rsp namespace in the aroma.core namespace solved this. Thanks Qian Liu for reporting on this.

Version: 2.3.1 [2011-11-11] o Added extractPSCNArray() for AromaUnitTotalCnBinary{File|Set}.

Version: 2.3.0 [2011-10-28] o Added a namespace to the package, which will be more or less a requirement starting with R v2.14.0.

Version: 2.2.2 [2011-09-29] o Added alpha version of the AromaRepository class.

Version: 2.2.1 [2011-09-24] o readHeader(), readRawFooter() and writeRawFooter() of AromaTabularBinaryFile would try to read non-signed 4-byte integers, which is not supported and would instead be read as signed integers. From R v2.13.1 this would generated warnings.

Version: 2.2.0 [2011-09-01] o Submitted to CRAN. o The package passes all redundancy tests.

Version: 2.1.5 [2011-08-30] o BUG FIX: After introducing a sanity check in aroma.core v2.1.2 (2011-05-11), getSnpPositions() of AromaCellSequenceFile would throw "Error: length(pos) == ncol(cells) is not TRUE". However, it was not until aroma.core v2.1.3 (2011-08-01) was release that some people got problem with this. It turns out that the sanity check catches an error in how getSnpPositions() of AromaCellSequenceFile allocates the result vector, a bug that has been there for a very long time. Luckily, this bug has had no effect on the results for anyone. Thanks to David Goode (Stanford) and Irina Ostrovnaya (MSKCC) for reporting on this.

Version: 2.1.4 [2011-08-02] o The aroma.core v2.1.3 tar ball uploaded to CRAN mistakenly contained a NAMESPACE file, which shouldn't have been there.

Version: 2.1.3 [2011-07-27] o WORKAROUND: In order for the package to work with the most recent version of R devel, which automatically add namespaces to packages who do not have one, we explicitly have specify that this package should use cat() and getOption() of R.utils (instead of 'base').

Version: 2.1.2 [2011-07-24] o Bumped up the package dependencies, especially since R will soon (in practice) require namespaces for all packages.

Version: 2.1.1 [2011-05-10] o ROBUSTNESS: Added more sanity checks and more verbose output to getSnpNucleotides() for AromaCellSequenceFile.

Version: 2.1.0 [2011-04-08] o No updates. Submitted to CRAN.

Version: 2.0.8 [2011-04-03] o CLEANUP: Utilizing hpaste() internally wherever applicable.

Version: 2.0.7 [2011-03-28] o BUG FIX: allocateFromUnitAnnotationDataFile() for AromaUnitTabularBinaryFile would include chip type tags in the path, e.g. annotationData/chipTypes/GenomeWidesSNP_6,Full.

Version: 2.0.6 [2011-03-14] o Now ChromosomeExplorer does a better job of listing chromosomes that are specific to the genome/organism used. o Added getChromosomeLabels() for ChromosomeExplorer.

Version: 2.0.5 [2011-03-04] o BUG FIX: lapplyInChunks(idxs) for numeric did not correctly handle the case when length(idxs) == 0, because of a typo.

Version: 2.0.4 [2011-03-03] o Added static loadAll() for SampleAnnotationSet. o Updated the default filename patterns used by findByGenome() for AromaGenomeTextFile to "^%s,chromosomes(|,.)[.]txt$". o Now getGenomeFile() for ChromosomalModel utilizes byGenome() for AromaGenomeTextFile to locate the genome annotation file. o GENERALIZATION: Now findByGenome() for AromaGenomeTextFile follows the new aroma search conventions. o GENERALIZATION: In addition to search // paths, findAnnotationData() can also search // by not specifying argument 'name' (or setting it to NULL). Also, if it cannot locate any files, it falls back to annotation data available in any of the aroma.* packages. o ROBUSTNESS: Added a return contract/sanity check asserting that getUnitsOnChromosomes() for AromaUnitChromosomeTabularBinaryFile truly returns valid 'unit' indices. Thanks to Emilie Sohier, France for reporting on a problem related to this.

Version: 2.0.3 [2011-03-02] o GENERALIZATION: Now the default for createImage() for matrix is to test to create images according to aroma settings option 'output/ImageClasses'. o GENERALIZATION: getAverageFile() for AromaUnitTotalCnBinarySet first searches for an existing result file according to the new search conventions. If not found, then it's created. o STANDARDIZATION: Now the default output path for all allocateFromUnitAnnotationDataFile() is annotationData/chipTypes//. Before it was the same directory as the original annotation data file, which may for instance have been in a deeper subdirectory, or recently also in a sibling root path. o ROBUSTNESS: Now getAverageFile() for AromaUnitTotalCnBinarySet creates the result file atomically by writing to a temporary file which is renamed afterward. o Now write() and read() for RasterImage throws an informative error message explaining that the 'png' package is needed. o BUG FIX: colorize() for Image would throw '<simpleError in ...: could not find function "colorMode">', because the colorMode() function needs to be explicitly imported after the recent package cleanups. o BUG FIX: colorize() for Image tried to call createImage() using a vector instead of a matrix. o BUG FIX: createImage() for matrix would not return the first possible image created (when testing different image classes) but instead continue trying to create image for all possible classes. For instance, this meant that although you had the 'EBImage' package installed, but not the 'png' package, it would still in the end try to (also) use 'png' package. If writing PNG images to file, say via ArrayExplorer, this would result in "Error in loadNamespace(name) : there is no package called 'png'". Thanks Richard Beyer at University of Washington for reporting on this.

Version: 2.0.2 [2011-02-19] o GENERALIZATION: Extended the default root paths of findAnnotationData() to be annotationData/ and annotationData,/

Version: 2.0.1 [2011-02-19] o CLEANUP: Moved static getTags() to Arguments to R.filesets v0.9.3. o CLEANUP: Deprecated static method importFromTable() for FileMatrix. o CLEANUP: Removed several deprecated methods.

Version: 2.0.0 [2011-02-16] o No updates. Submitted to CRAN.

Version: 1.9.4 [2011-02-07] o CLARIFICATION: Now the exception thrown by getRawCopyNumbers() for CopyNumberSegmentationModel, when there are too many non-finite signals, gives a more informative error message containing information also on which sample, reference and chromosome the problem was detected on. o BUG FIX: Now fit() for CopyNumberSegmentationModel passes down argument 'maxNAFraction' to the internal sanity test as it used to do before aroma.core v1.3.4 (November 2009).

Version: 1.9.3 [2011-02-01] o GENERALIZATION: Now spatial PNG image files can also be created utilizing the 'png' package as an alternative to the 'EBImage' package. The EBImage package can be tricky to install on some OSes, e.g. Windows 7 64-bit. o Added alpha version of an internal RasterImage class. o Added an internal writeImage() for Image objects as defined by the EBImage package. This made it possible to remove the remaining explicit dependencies on EBImage in the aroma.affymetrix package. o ROBUSTNESS: Removed some remaining partial argument calls. o CLEAN UP: Removed deprecated internal rgbTransform() for Image. o CLEAN UP: Deprecated internal as.TrueColorImage() for the Image class and for matrices.

Version: 1.9.2 [2011-01-30] o SPEED UP: The memoization/caching mechanisms should now be faster on Windows, because digest() uses the faster serialize() of R v2.12.0. The earlier version was orders of magnitude slower on Windows, which we have been patching in the aroma framework since v0.9.3.4. That patch wrote to file, which was slower than the recent fix. This Windows-only patch is no longer needed, and hence neither applied, on R v2.12.0 and beyond.

Version: 1.9.1 [2011-01-14] o Added argument 'flavor' to segmentByGLAD() for RawGenomicSignals, which makes it possible to specify whether daglad() or glad() of the GLAD package will be used. The 'flavor' argument can also be passed as for instance GladModel(..., flavor="daglad").

Version: 1.9.0 [2011-01-10] o No updates. Submitted to CRAN.

Version: 1.8.3 [2010-12-27] o Added genome annotation file Mouse,chromosomes.txt to system.file("annotationData/genomes/Mouse", package="aroma.core").

Version: 1.8.2 [2010-12-07] o ROBUSTNESS: Whenever the GLAD package is tried to be loaded and it fails due to failure of loading a shared library, then this will be remembered for 24 hours while it will not be loaded again. o Added requireWithMemory().

Version: 1.8.1 [2010-12-02] o BUG FIX: plot() for CopyNumberSegmentationModel would throw exception "Cannot infer number of bases in chromosome. No such chromosome: 25" for chromosome 25. o BUG FIX: drawCytoband2() would throw an error if argument 'cytoband' was an empty data frame, which could happen if there is no cytoband annotation data for the requested chromosome. Now it returns quietly.

Version: 1.8.0 [2010-11-07] o Committed to CRAN. o CLEANUP: Dropped non-used Javascript toolkit code that was intended to be used for a future version of ChromosomeExplorer.

Version: 1.7.6 [2010-11-06] o ROBUSTNESS: Now subsample() for BinnedScatter utilizes resample(). o CLEANUP: Removed stext(). It is in R.utils. o CLEANUP: Removed some outdated patches for R v2.7.0 and before. o CLEANUP: Package no longer need to "suggest" geneplotter.

Version: 1.7.5 [2010-10-25] o Now fit() for CopyNumberSegmentationModel also passed the optional arguments ('...') passed to the constructor function. This makes it possible to specify all arguments while initiating the model, e.g. sm <- CbsModel(..., min.width=5, alpha=0.05). o Now optional arguments '...' to CopyNumberChromosomalModel are recorded.

Version: 1.7.4 [2010-10-13] o ROBUSTNESS/BUG FIX: The internal drawCytoband2() used to annotate chromosomal plots with cytobands tries to utilize GLAD package, if available. However, even when GLAD is installed it may still be broken due to missing dynamic libraries, e.g. 'Error in library.dynam(lib, package, package.lib) : DLL 'GLAD' not found: maybe not installed for this architecture?'. We now avoid this too.

Version: 1.7.3 [2010-09-12] o Added drawDensity() for CopyNumberRegions and RawGenomicSignals. o Added getDensity() for CopyNumberRegions which returns the empirical density of the mean levels weighted by the region lengths. o Added getLength() for CopyNumberRegions, which returns a vector of region lengths. o Now the ylim defaults to c(0,5) for plot() for RawCopyNumbers. o Added basic support for operators +, - and * to RawGenomicSignals.

Version: 1.7.2 [2010-08-22] o Added the AromaGenomeTextFile class. o Added genome annotation file Canine,chromosomes,UGP,HB20100822.txt to system.file("annotationData/genomes/Canine", package="aroma.core"). o BUG FIX: annotationData/genomes/Human/Human,chromosomes.txt had an extra TAB on the ChrM row.

Version: 1.7.1 [2010-08-06] o Added abstract classes SegmentationDataFile and SegmentationDataSet to represent segmentation data results. Current subclasses are CbsSegmentationData(File|Set). o Added more utility methods for CopyNumberRegions.

Version: 1.7.0 [2010-07-26] o Committed to CRAN. No updates.

Version: 1.6.8 [2010-07-24] o Added several methods for CopyNumberRegions, e.g. xRange(), prune(), simulateRawCopyNumbers(), "+"(), "-"() and "*"().

Version: 1.6.7 [2010-07-20] o Added writeDataFrame() for AromaUnitTotalCnBinarySet and AromaUnitFracBCnBinarySet to get the correct filename extension. Thanks Nicolas Vergne at the Curie Institute for reporting this.

Version: 1.6.6 [2010-07-19] o Added subset() for CopyNumberRegions. o Now extractRegion() for RawGenomicSignals also accepts a CopyNumberRegions object for argument 'regions'. o Added extractRegions() for RawGenomicSignals.

Version: 1.6.5 [2010-07-08] o BUG FIX: writeDateFrame() for AromaUnitSignalBinarySet would write the same data chunk over and over.

Version: 1.6.4 [2010-07-06] o BUG FIX: indexOf() for ChromosomalModel would return NA if a search pattern contained parenthesis '(' and ')'. There was a similar issue in indexOf() for GenericDataFileSet/List in R.filesets, which was solved in R.filesets 0.8.3. Now indexOf() for ChromosomalModel utilizes ditto for GenericDataFileSet for its solution.

Version: 1.6.3 [2010-06-22] o BUG FIX: as.GrayscaleImage(..., transforms=NULL) for 'matrix' would throw "Exception: Argument 'transforms' contains a non-function: NULL".

Version: 1.6.2 [2010-06-02] o BUG FIX: updateDataColumn() of AromaTabularBinaryFile would censor signed integers incorrectly; it should censor at/to [-(n+1),n], but did it at [-n,(n+1)] ("two's complement"). This caused it to write too large values as n+1, which then would be read as -(n+1), e.g. writing 130 would be censored to 128 (should be 127), which then would be read as -128. Added more detailed information on how many values were censored. Thanks Robert Ivanek for report on this.

Version: 1.6.1 [2010-05-27] o Added trial version of fullname translator files. o doCBS() for character:s support data set tuples. o Added doCBS() for CopyNumberDataSetTuple:s.

Version: 1.6.0 [2010-05-14] o Package submitted to CRAN. o Package pass R CMD check on R v2.11.0 and v2.12.0 devel.

Version: 1.5.8 [2010-05-13] o Now argument 'path' of all writeDataFrame() methods defaults to ,txt///.

Version: 1.5.7 [2010-04-27] o Added writeDataFrame() for AromaUnitTabularBinaryFile. o Added argument 'columnNamesPrefix' to all writeDataFrame(). o AD HOC: Now getUnitAnnotationDataFile() of AromaPlatformInterface load aroma.affymetrix if needed and if installed.

Version: 1.5.6 [2010-04-22] o Added writeDataFrame() for AromaUnitSignalBinary{File|Set}.

Version: 1.5.5 [2010-04-12] o BUG FIX: getFitFunction() of CbsModel would return a function that would give "Error in segmentByCBS.RawGenomicSignals(..., seed = seed): formal argument "seed" matched by multiple actual arguments".

Version: 1.5.4 [2010-04-06] o Added equals() for CopyNumberRegions. o Added argument 'seed' to CbsModel, which will, if specified, set the random seed (temporarily) each time (per sample and chromosome) before calling the segmentation method.

Version: 1.5.3 [2010-04-05] o Added argument 'seed' to segmentByCBS() for RawGenomicSignals.

Version: 1.5.2 [2010-03-29] o ROBUSTNESS: Increased the requirements of support packages.

Version: 1.5.1 [2010-03-02] o Now segmentByMPCBS() can be used to segment data from a single source. o CHANGE: Argument 'arrays' of doCBS() for CopyNumberDataSet no longer subset the input data set, but instead is passed to the fit() function of the segmentation model. This way all arrays in the input data set are still used for calculating the pooled reference. o ROBUSTNESS: Added more sanity checks to segmentByMPCBS() for RawGenomicSignals. o BUG FIX: Forgot argument 'verbose' of getOutputSet() of ChromosomalModel.

Version: 1.5.0 [2010-02-22] o Submitted to CRAN. No changes since v1.4.7. o Package passes R CMD check on R v2.10.1 patch and R v2.11.0 devel. o Package passes all redundancy tests.

Version: 1.4.7 [2010-02-21] o Added the AromaCellCpgFile class. o Added Rd help for AromaCellPositionFile class.

Version: 1.4.6 [2010-02-19] o SIMPLIFICATION: Now it is possible to use ChromosomeExplorer without having to install the GLAD package (used before for cytobands). o SIMPLIFICATION: Now it is possible to plot cytobands without having to install the GLAD package. o Argument 'zooms' of ChromosomeExplorer now default to 2^(0:6), instead of 2^(0:7), because the images for zoom 2^7=128 would not display in Firefox for the largest chromosomes. o Updated getGenomeFile() for ChromosomalModel such that it can be used to locate other types of genome annotation files as well, files that may be optional (without giving an error). o Added Human cytoband files to annotationData/genomes/. o Added annotationData/genomes/ to aroma.core (from aroma.affymetrix). o Added getOutputSet() for ChromosomalModel. o Added alpha version of a doCBS().

Version: 1.4.5 [2010-02-10] o ROBUSTNESS: Now also patches for R.filesets and R.utils are loaded, if available, when aroma.core is loaded. o CLEANUP: Removed debug print() statements in isCompatibleWith().

Version: 1.4.4 [2010-02-03] o ROBUSTNESS: Package now requires matrixStats v0.1.9 or newer, due to a bug in the earlier versions that would affect smoothing of chromosomal signals that contains missing values. o Package passes R CMD check and all redundancy tests.

Version: 1.4.3 [2010-01-25] o ROBUSTNESS: Added a sanity check getChromosomes() for class AromaUnitChromosomeTabularBinaryFile validating that the file has a 'chromosome' column. o CLEANUP: Using new Arguments$getTags() where ever possible.

Version: 1.4.2 [2010-01-13] o ChromosomalModel:s (and and the ChromosomeExplorer) no longer require unit names files. o getListOfAromaUgpFiles() for ChromosomalModel no longer goes via getListOfUnitNamesFiles(). This opens up the possibility to work with data files without unit names files, e.g. smoothed CN data. o Added getAromaUgpFile() for AromaPlatformInterface. o Now getUnitNamesFile() for AromaPlatformInterface utilizes the generic getUnitAnnotationDataFile() method.

Version: 1.4.1 [2010-01-06] o Added argument 'defaults' to allocate() of AromaTabularBinaryFile.

Version: 1.4.0 [2010-01-04] o Added trial version of segmentByMPCBS() via the 'mpcbs' package. o BUG FIX: Added getDefaultFullName() for AromaMicroarrayDataSet and AromaTabularBinarySet in order to override (parent=1) the new default of GenericDataFileSet in R.filesets v0.7.0, which would return the chip type (parent=0) as the name. o Package passes R CMD check on R v2.10.1 and R v2.11.0 devel and all of its redundancy tests.

Version: 1.3.8 [2010-01-02] o Added getPairedNames() to CopyNumberChromosomalModel which returns combined 'vs' names, e.g. 'TumorvsNormal'. The default behavior is that if is the average of a pool, then the paired name is '', e.g. 'Tumor'. o CLEAN UP: Moved all GenericSummary code to R.utils.

Version: 1.3.7 [2010-01-01] o Added argument 'pattern' to byName() for AromaUnitTotalCnBinarySet and AromaUnitFracBCnBinarySet. o getSets() of AromaMicroarrayDataSetTuple overrides the default method by adding the chip types as the names of the returns list. o CLEAN UP: Removed getSetTuple() from ChromosomeExplorer. o ROBUSTNESS: Using new Arguments$getInstanceOf() were possible. o ROBUSTNESS: Now CopyNumberChromosomalModel() asserts that none of the test samples have duplicated names. o ROBUSTNESS: Now all index arguments are validated correctly using the new 'max' argument of Arguments$getIndices(). Before the case where "max == 0" was not handled correctly. o BUG FIX: translateFullNames() of ChromosomeExplorer would translate the full names, but return the original ones. o BUG FIX: getFullNames() of ChromosomeExplorer reported: Error in UseMethod("translateFullNames") : no applicable method for 'translateFullNames' applied to an object of class "character".

Version: 1.3.6 [2009-12-08] o BUG FIX: extractMatrix() of AromaUnitCallFile did not recognize NoCalls.

Version: 1.3.5 [2009-12-02] o BUG FIX: extractRawCopyNumbers() for RawCopyNumbers would give an error if the internal logBase was NULL.

Version: 1.3.4 [2009-11-24] o Moved ChromosomeExplorer to aroma.core from aroma.affymetrix. o Moved several method for 'profileCGH' objects to aroma.core from aroma.affymetrix. o Added extractRawCopyNumbers(, ...logBase=2) to RawCopyNumbers, which can be used to change the logarithmic base of CN ratios, if any. o Added getAverageFile() for AromaUnitTotalCnBinarySet. o Now all chromosome plot functions have xScale=1e-6 by default.

Version: 1.3.3 [2009-11-19] o ALPHA: First successful run of segmentation with CbsModel with AromaUnitTotalCnBinarySet data sets. o Added isAverageFile() for AromaUnitSignalBinaryFile. o Added class AromaUnitTotalCnBinarySetTuple. o GENERALIZATION: Moved CbsModel, GladModel and HaarSegModel (all segmentation models) of aroma.affymetrix to here. o GENERALIZATION: Moved all (generalized) ChromosomalModel, CopyNumberChromosomalModel, and CopyNumberSegmentationModel from aroma.affymetrix to here. o Added interfaces CopyNumberDataFile, CopyNumberDataSet, and CopyNumberDataSetTuple (internal for now).

Version: 1.3.2 [2009-11-12] o Now AromaUflFile$allocateFromUnitNamesFile() works. o Added getAromaUflFile() to UnitAnnotationDataFile. o Moved AromaUflFile to aroma.core (from aroma.affymetrix). o BUG FIX: importFrom(ufl, dat, ...) where 'ufl' was an AromaUflFile and 'dat' a GenericTabularFile gave an error reporting that importFromGenericTabularFile() is abstract/not defined for AromaUflFile:s. Thanks Paolo Guarnieri for reporting this.

Version: 1.3.1 [2009-11-03] o Replaced Rd cross references to sfit and HaarSeg packages with plain text in order to meet the CRAN requirements that all Rd links must exist on the CRAN servers.

Version: 1.3.0 [2009-11-01] o New public release. o More recent dependencies on Bioconductor packages. o Package passes R CMD check on R v2.10.0 and all redundancy tests.

Version: 1.2.3 [2009-10-25] o Added getExtensionPattern() to most GenericDataFile classes.

Version: 1.2.2 [2009-10-16] o Added setName() for RawGenomicSignals. o Stricter dependencies.

Version: 1.2.1 [2009-10-02] o CLEAN UP: Updated to use byPath() instead fromFiles(). o CLEAN UP: Move the Interface class to the R.oo package.

Version: 1.2.0 [2009-09-09] o New public release. o Fixed broken/missing Rd links. o Package passes R CMD check on R v2.9.2 and all redundancy tests.

Version: 1.1.7 [2009-09-07] o Now getUnitsOnChromosomes() for AromaUnitChromosomeTabularBinaryFile returns a vector by default (unlist=TRUE).

Version: 1.1.6 [2009-09-07] o Added yRange(), yMin() and yMax() for RawGenomicSignals. o Added extractRawCopyNumbers() for RawSequenceReads. o BUG FIX/WORKAROUND: smoothScatter(), which is used in for instance aroma.affymetrix, is in the graphics package from R v2.9.0. It was previously in geneplotter v1.2.4 and before(!). The code imported it from geneplotter would therefore give an error of a missing function with geneplotter v1.2.5. We are now assuming R v2.9.0 by default, but if not available, but geneplotter v1.2.4 or earlier is, geneplotter is loaded. If neither are available, a dummy smoothScatter() is setup reporting an error.

Version: 1.1.5 [2009-08-29] o Added totalAndFracBData/ to the search path of byName() for AromaUnit(FracB|Total)CnBinarySet.

Version: 1.1.4 [2009-07-22] o Added allocateFromUnitAnnotationDataFile() for AromaUnitSignalBinaryFile and AromaUnitTabularBinaryFile. o Added getUnitTypesFile() for AromaPlatform and AromaPlatformInterface. o Added UnitAnnotationDataFile, which now the UnitNamesFile and the new UnitTypesFile inherits from. o Now uses() for Interface takes multiple Interface:s.

Version: 1.1.3 [2009-07-03] o Added class RawSequenceReads. o Added support for argument 'byCount' to binnedSmoothingByState() of SegmentedCopyNumbers. It is rather complex how it works, but we tried to immitate how it works with byCount=FALSE. o Now binnedSmoothing() of RawGenomicSignals demark locus fields that were not binned to be regular fields. Ideally all locus fields (including custom ones) should be binned, but we leave that for a future implementation. o Added get-, setStateColorMap(), and getStateColors() for class SegmentedGenomicSignalsInterface.

Version: 1.1.2 [2009-06-14] o Added argument keepUnits=FALSE to extractRawGenomicSignals() of AromaUnitSignalBinaryFile. o Now RawGenomicSignals(y=rgs) sets all locus fields in 'rgs' if it is a RawGenomicSignals object. o BUG FIX: exportTotalCnRatioSet() would return a AromaUnitFracBCnBinarySet. o Updated examples() that requires "suggested" packages to be ran conditionally, so that it does not throw an error (in R CMD check) if the packages is not available. This is required for a package to be put on CRAN.

Version: 1.1.1 [2009-06-10] o ADDED: Added support for "birdseed" encoding in extractGenotypes() and updateGenotypes() of AromaUnitGenotypeCallFile. o SPEED UP: updateGenotypes() of AromaUnitGenotypeCallFile is now much faster in counting A:s and B:s. o Added SegmentedGenomicSignalsInterface, which implements all the methods for SegmentedCopyNumbers and the new SegmentedAlleleBFractions. o Added getFields() to Interface as an ad hoc solutions to avoid print() throwing 'Error in UseMethod("getFields") : no applicable method for "getFields"'. o GRAMMAR FIX: is(Homo|Hetero)zygous(), not is(Homo|Hetero)zygote(). o BUG FIX: isHomozygote() of AromaUnitGenotypeCallFile was not correct. o BUG FIX: getOutputDataSet() of AromaTransform failed to identify the output files if (and only if) a filename translator was applied to the input data set.

Version: 1.1.0 [2009-05-29] o New public release. No updates. o Package passes R CMD check on R v2.9.0 and all redundancy tests.

Version: 1.0.8 [2009-05-25] o GENERALIZATION: The AromaTransforms class was generalized further to handle cases where the number of output files does not map one to one to the input files.

Version: 1.0.7 [2009-05-18] o Added extractRawAlleleBFractions() for AromaUnitFracBCnBinaryFile. o Added exportFracBDiffSet() for AromaUnitFracBCnBinarySet. o Moved the Explorer class and its support files under inst/ from aroma.affymetrix to aroma.core. o Moved the AromaCellPositionFile class from aroma.affymetrix to aroma.core. o ADDED: Now all segmentByNnn() for RawGenomicSignals also returns so called 'aromaEstimates', which are additional parameter estimates, e.g. robust estimates of the standard deviation of all full-resolution CNs as well as per identified region. o CLEAN UP: Moved all file set specific classes and methods to the new R.filesets package. o MEMORY OPTIMIZATION: Where ever possible/applicable, we now use Arguments$getNumerics(), which, in R utils v1.1.5 and new, corces to doubles only if the input is not already doubles. This will lower the memory usage in some cases since an integers use 4 bytes and doubles 8 bytes. This also save disk space if object is saved to disk, e.g. a DNAcopy fit object with integer genomic positions instead of double ones, save approx 5-7% disk space. o ROBUSTNESS: Now allocate() for AromaTabularBinaryFile first allocates a temporary file which is then renamed. This makes the file allocation more atomic, and therefore less error prone to interrupts etc. o ROBUSTNESS: Now indexOf() for UnitNamesFile assert that exactly one of the 'pattern' and 'names' arguments is given. It also gives an informative error message if 'pattern' is a vector. o ROBUSTNESS: Now all arguments that are expected to be exactly one character string (not an empty vector or a vector of length two) are asserted to be that too. This closes some potential bugs. o EXCEPTION HANDLING: All methods that modifies an existing file, are now asserting that the file permissions allow modifying it, and if not gives a clear error message that this is the case. o BUG FIX: allocateFromUnitNamesFile() for AromaUnitSignalBinaryFile would not call generic allocate() but the one for this class. o BUG FIX: extractMergedRawCopyNumbers(..., unshift=TRUE) would estimate the relative shifts between platforms using smoothed CNs over the genomic region defined by the first data set. Now it is done over the region defined by the union of all data sets. The impact of this bug should be neglectable or zero.

Version: 1.0.6 [2009-05-14] o Now binnedSmoothing() of RawGenomicSignals uses weighted estimates (by default) if weights exists. o Added RawAlleleBFractions() extending RawGenomicSignals. o Added extractCopyNumberRegions() for profileCGH, DNAcopy, and HaarSeg segmentation object. Before they were in aroma.affymetrix. o Added segmentByCBS(), segmentByGLAD(), and segmentByHarSeeg() to RawGenomicSignals, which all support weights if the underlying segmentation method does. To date, it is only CBS and HaarSeg that supports weights. These methods also support memoization. o Added extractRegion() to RawGenomicSignals. o Added getWeights() and hasWeights() to RawGenomicSignals. o Added {add,subtract,multiply,divide}By() for RawGenomicSignals all utilizing support method applyBinaryOperator(). o ALPHA: Added classes GenericDataFile{Set}List. o ALPHA: Added class AromaUnitTotalCnBinaryFileList with methods extractRawCopyNumbers() and extractMergedRawCopyNumbers(). o SPEED UP: Now TextUnitNamesFile caches all unit names in memory. o BUG FIX: Now aroma.core works with the IRanges and grid packages, regardless on the order they were loaded. o BUG FIX: getPlatform() of TextUnitNamesFile would sometimes return a list of length one, instead of an single character string. o BUG FIX: extractSubset() of RawGenomicSignals did not recognize all locus fields.

Version: 1.0.5 [2009-05-10] o Now getOutputDataSet() of AromaTransform returns a data set with files ordered such that the fullnames are ordered the same way as the input data set. Suggested by Xin (Victoria) Wang at UC Berkeley. o Now getOutputDataSet() of AromaTransform scans for the output data files with fullnames matching those of the input data set. This is one step closer to being able to batch process subsets of data sets when the method is, say, a single-array method. o Now static fromFiles() of GenericDataFileSet supports empty data sets. o Now readDataFrame() of AromaUgpFile and AromaUnitTabularBinaryFile accepts rows=integer(0). o Added abstract class AromaUnitChromosomeTabularBinaryFile to make it easier to setup up new annotation file formats based on chromosomes. AromaUgpFile is now inheriting from this class. getUnitsOnChromosomes() now returns a list stratified by chromosome. o Added extractByChromosomes() for AromaUgpFile. o Added argument 'translate' to getColumnNames() of TabularTextFile. o UPDATE: Replace argument 'robust' of colBinnedSmoothing() with a more generic 'FUN' argument. The default arguments give identical results. o BUG FIX: Our internal interleave() for Image (defined by EBImage) gave 'Error in z[idxOdd,, ] : incorrect number of dimensions'. This was because internal image structure of the Image class changed (back) to being a 2-dim array. Now interleave() handles both 2d and 3d arrays. o BUG FIX: lines() of RawGenomicSignals did not recognize x/yScale. o BUG FIX: as.character() of GenericDataFile would throw 'Error in sprintf("%d", getFileSize(db, "numeric")) : use format %f, %e, %g or %a for numeric objects' whenever the file size is returned as a double, which happens for very large files (> 2^31-1 bytes). o BUG FIX: as.character() of GenericDataFileSet would throw an error if the data set was empty, because then there was no path. o Package passes R CMD check on R v2.9.0.

Version: 1.0.4 [2009-04-07] o BUG FIX: getUnitNames(..., units=NULL) of TextUnitNamesFile would make the object believe there are zero units in the file. Thanks Shermane Teo at the National University of Singapore for reporting this. o BUG FIX: binnedSmoothing(..., byCount=TRUE) of RawGenomicSignals would give error "[...] object "ys" not found". o BUG FIX: When passing a single data points to colBinnedSmoothing(), it would throw the exception: "Range of argument 'by' is out of range [0,0]: [,]".

Version: 1.0.3 [2009-03-23] o Added the TextUnitNamesFile class.

Version: 1.0.2 [2009-02-26] o Added argument 'units' to extractRawCopyNumbers() of AromaUnitSignalBinaryFile. o Added RawGenomicSignals which RawCopyNumbers now inherits from. o Added readDataFrame(..., units=NULL) to AromaUnitSignalBinaryFile. o Added optional argument/field 'name' to RawCopyNumbers, which is also used by SegmentedCopyNumbers when querying the "truth" function(s) for the copy-number state. This makes it possible to use one (conditional) truth functions for all samples. o Added hasBeenModified() to GenericDataFile. o Now hasTags(..., tags) of GenericData{File|Set} splits the 'tags' argument. o Now RawCopyNumbers() takes RawCopyNumbers objects as input. o Now getChecksum() of GenericDataFile caches results unless the file has been modified since last time. o Now as.character() of GenericDataFile also reports the exact file size in case the file size is reported in kB, MB, etc. It also tries to report the relative pathname rather than the absolute.

Version: 1.0.1 [2009-02-12] o Now byName() of AromaUnit(FracB|Total)CnBinarySet searches rawCnData/ then cnData/. o Added SegmentedCopyNumbers class. o Added various smoothing methods to RawCopyNumbers. o Added colBinnedSmoothing() and colKernelSmoothing(). o Added getAromaUgpFile() to UnitNamesFile. o Added shakyText(). o Added static byChipType() to UnitNamesFile. o Added argument 'fullname' to getChipType() of AromaUnitSignalBinaryFile. o Now argument 'files' in extract() of GenericDataFileSet can also be a vector of string. o ROBUSTNESS: Added support for optional validation/selection by the number of units/cells to all static byChipType() methods. This is done by specifying argument nbrOfUnits/nbrOfCells. This is intend for internal use only. o ROBUSTNESS: Added a sanity check to getAromaUgpFile() of UnitNamesFile and AromaUnitSignalBinaryFile, which asserts that the number of units in the located UGP file match that the number of units in the data file. o ROBUSTNESS: Now findAnnotationData() always returns pathnames ordered by the length of their fullnames. Before this was only done if 'firstOnly=TRUE'. o ALPHA: Added support for "smart" (e.g. "*") subdirectories in static findByName() of GenericDataFileSet.

Version: 1.0.0 [2009-01-12] o Added getMaxLengthRepeats() to AromaCellSequenceFile. o Added AromaUnitSignalBinary{File|Set}, AromaUnitTotalCnBinary{File|Set}, AromaUnitFracBCnFinary{File|Set}, AromaUnitCall{File|Set}, and AromaUnitGenotypeCall{File|Set}. o BUG FIX: readFooter() of AromaTabularBinaryFile did not return the correct list for nested structures. o BUG FIX: groupBySnpNucleotides() of AromaCellSequenceFile would return an empty element 'missing' for some chip types, e.g. Mapping10K_Xba142. Now that empty elements are dropped. o BUG FIX: getAttributes() for GenericDataFile:s would give an error if there were no attributes.

Version: 0.9.6 [2008-12-04] o SPEED UP: Now predict() of ProbePositionEffects is 6-7 times faster. o SPEED UP: Now the result of isMissing() for AromaCellSequenceFile can be cached. o ALPHA: Added the BinnedScatter class with methods. o CLEAN UP: readDataFrame() of AromaTabularBinaryFile would forget to close the connection if verbose output was activated. When R later would close such connections, a warning would be generated.

Version: 0.9.5 [2008-10-17] o Package passes R CMD check on R v2.7.2 and R v2.8.0rc.

Version: [2008-10-16] o BUG FIX: Tried to turn a function passed to as.GrayscaleImage() in argument 'transforms' to a list using as.list() and not list().

Version: [2008-09-18] o Added argument 'skip' to writeChecksum() of GenericDataFile.

Version: [2008-09-03] o Added getSnpPositions(), getSnpShifts(), getSnpNucleotides() and groupBySnpNucleotides() to AromaCellSequenceFile.

Version: [2008-08-31] o Update fitGenotypeCone() to support both flavors 'sfit' (old) and 'expectile' (new).

Version: [2008-08-12] o Added support for argument 'positions' to countBases() for AromaCellSequenceFile. o ALPHA: Added fitMultiDimensionalCone(). o BUG FIX: readSequences() for AromaCellSequenceFile translated raw values to incorrect nucleotides. o TESTING: Added redundancy tests to aroma.core.

Version: 0.9.4 [2008-08-02] o Public release. Package passes R CMD check on R v2.7.1 and R v2.8.0 devel on WinXP.

Version: [2008-07-24] o SPEED UP: Added patch for base::serialize() on Windows, which in turn will speed up digest::digest() and all methods that use the latter to generate hashcodes. o SPEED UP: Now as.character() for GenericTabularFile:s and TabularTextFile:s reports the number of data rows and the number of text lines as NA if the files are too large and cached results are not already available. o SPEED UP: Replaced all which() with faster whichVector(). o Added getCreatedOn(), getLastModifiedOn(), and getLastAccessedOn() to GenericDataFile. These a just wrapper accessing fields.

Version: [2008-07-21] o Now countBases() of AromaCellSequenceFile returns "raw" counts if argument 'mode="raw"'. o Now updateDataColumn() coerce values to doubles before censoring them for raw and integer columns. o Now findByName() assert that the data set name is not empty. o ALPHA: Added setFullName() and setName() to GenericDataFile and GenericDataFileSet. The plan is to have these replace what getAlias() and setAlias() do today. o BETA: Added setFullNameTranslator() to GenericDataFileSet.

Version: [2008-07-16] o BETA: Added setFullNamesTranslator() (for the files) to AromaGenericFileSet. o ALPHA: Added protected update2() to GenericDataFileSet. o ALPHA: Added private ProbePositionEffects et al.

Version: [2008-07-12] o SPEED UP: Now all AromaTabularBinaryFile:s, such as AromaUgpFile, read data much faster after two modifications to readDataFrame(): (i) rownames are no longer generate, if not asked for explicitly, and (ii) garbage collection is no longer done after each column. o Added a general importFrom() for AromaTabularBinaryFile, which calls matching importFrom(), if found. o Added support for 'raw' data columns in AromaTabularBinaryFile. o BETA: Added readTableHeader(). o BETA: Added AromaCellSequenceFile. o BETA: Added classes AromaMicroarrayTabularBinaryFile and AromaCellTabularBinaryFile.

Version: 0.9.3 [2008-06-08] o Package passes R CMD check on R v2.7.0 patched.

Version: [2008-06-07] o Update filename pattern for getOutputFiles() of AromaTransform.

Version: [2008-05-25] o Added AromaTransform (extracted from aroma.affymetrix::Transform). o Added nbrOfArrays() to AromaMicroarrayDataSet. o Now private xmlToList() handles more complex XML strings.

Version: [2008-05-22] o Added member 'chromosome' to RawCopyNumbers. o Added gaussianSmoothing() to RawCopyNumbers. o Added argument 'xOut' to gaussianSmoothing() in order to specify at what loci the smoothed signals should be calculated.

Version: [2008-05-21] o Now findPngDevice() search for a working PNG device in the following order: png(..., type="cairo"), png(..., type="cairo1"), Cairo::CairoPNG(), R.utils::png2(), and finally plain png(). o Added gzip()/gunzip() to GenericDataFile. o Added static findByName() and byName() to GenericDataFileSet. o Added static getFileClass() to GenericDataFileSet. This makes it possible to remove most fromFiles() from subclasses but also the validation of argument 'files' of their constructors. o Added validate() to GenericDataFileSet, which is called at the end of fromFiles(..., .validate=TRUE). o Added extractMatrix to GenericTabular(File|Set) and AromaTabularBinary(File|Set). o Added equals() and hasFile() to GenericDataFileSet. o Added classes GenericTabularFileSet and AromaTabularBinarySet. o Added stextChipType() for strings. o CLEAN UP: Moved more classes and methods from aroma.affymetrix to aroma.core: RawCopyNumbers, CopyNumberRegions, CopyNumberOutliers. Moved attribute methods from AffymetrixCel{File|Set} to AromaMicroarrayDataSet. Moved stextNnn() methods from AffymetrixFile to AffymetrixMicroarrayDataSet. Created superclass AromaMicroarrayDataSetTuple of AffymetrixCelSetTuple. o BUG FIX: readDataFrame() did not read the first data row if there was no column header; it was eaten up by a preceeding readHeader(). o BUG FIX: findAnnotationDataByChipType(chipType="GenomeWideSNP_6", pattern="^GenomeWideSNP_6.*[.]ugp$") would find file 'GenomeWideSNP_6,Full,na24.ugp' before 'GenomeWideSNP_6,na24.ugp'. Now we return the one with the shortest full name. o ALPHA: Now equals() for GenericDataFile:s uses the class, pathname, file size and file-contents checksum to do the comparison. Similarly, for GenericDataFileSet:s, the class, path, number of files, pathnames, and finally equals() for each file pair is used for the comparison. o ALPHA: Added full name translation for GenericDataFile:s. o ALPHA: Added UnitNamesFile. o Package passes R CMD check on R v2.7.0 patched.

Version: 0.9.2 [2008-05-10] o Took all core classes and core methods in aroma.affymetrix that are independent of the Affymetrix platform and placed the here. o The version is numbered starting from the current version of aroma.affymetrix. o BUG FIX: interleave() for Image gave 'Error in z[idxOdd, ] : incorrect number of dimensions'. The internal image structure is a 3-dim array. o BUG FIX: When searching with 'firstOnly=FALSE', findAnnotationData() was identifying files that are in "private" directory. This is how affxparser::findFiles() works. Such files are now filtered out. o Created.

Reference manual

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3.1.1 by Henrik Bengtsson, 2 months ago,

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Authors: Henrik Bengtsson [aut, cre, cph], Mark Robinson [ctb], Ken Simpson [ctb]

Documentation:   PDF Manual  

LGPL (>= 2.1) license

Imports stats, utils, R.methodsS3, R.oo, R.cache, R.rsp, matrixStats, RColorBrewer, PSCBS, listenv, future

Depends on R.utils, R.filesets, R.devices

Suggests KernSmooth, png, Cairo, EBImage, preprocessCore, aroma.light, DNAcopy, GLAD, sfit, expectile, HaarSeg, mpcbs

Imported by ACNE.

Depended on by NSA, aroma.affymetrix,, calmate.

See at CRAN