writeDataFrame() of AromaUnitSignalBinaryFile and
AromaUnitTabularBinaryFile.Removed defunct method whatDataType().
The segmentByMPCBS() method does not work in R
(>= 4.2.0). This is because the mpcbs package has
_R_CHECK_LENGTH_1_CONDITION_
and_R_CHECK_LENGTH_1_LOGIC2_ bugs, which give errors in R
(>= 4.2.0). The mpcbs package is a legacy package
that is no longer maintained. Because of this, it is likely that
segmentByMPCBS() and support for MPCBS segmentation will
eventually be dropped from aroma.core.
downloadFile() for AromaRepository is now smarter about
*.gz files.Re-export S3 generic process() from
R.rsp.
Argument pattern for findByGenome() for
AromaGenomeTextFile has an sprintf() mistake causing it to
produce a warning in R (>= 4.1.0).
WORKAROUND: Package fails R CMD check with
_R_CHECK_LENGTH_1_LOGIC2_=true due to PR#17663
(https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17663). Made a
simple code tweak to avoid this bug hitting us.
WORKAROUND: There’s a _R_CHECK_LENGTH_1_LOGIC2_ bug
in mpcbs::mpcbs.mbic(). Until fixed, we need to disable
this check while testing segmentByMPCBS().
findByChipType() for AromaMicroarrayTabularBinaryFile
and TextUnitNamesFile would only recognize Windows Shortcut Links with a
filename extension in lower case (*.lnk) but not in upper
case (*.LNK).extract() from R.utils
instead of R.filesets, which would result in
R CMD check errors for aroma.affymetrix
with R-devel (>= 3.6.0).getRegions() for CopyNumberSegmentationModel used
future strategy eager that is defunct in
future (>= 1.6.0) - updated to
sequential.Now file sizes are reported using IEC binary prefixes, i.e. bytes, KiB, MiB, GiB, TiB, …, YiB.
Now genomic positions / distances are reported in ‘Mbp’ (was ‘MB’ and ‘Mb’).
Objects no longer report on memory (RAM) usage.
Package used %<=% internally with was deprecated
in future (>= 1.4.0).
exportTotalCnRatioSet() for
AromaUnitTotalCnBinarySet and exportFracBDiffSet() for
AromaUnitFracBCnBinarySet would return files with file names matching
.asb, which would incorrectly also include
.asb.md5 files. Thanks to Thomas Grombacher at the Merck
Group for the report.
Default method whatDataType() is now
defunct.
Argument .old of getChipType() for
AromaMicroarrayTabularBinaryFile is now defunct (was deprecated in
2008!).
Previously deprecated argument maxNAFraction to
getRawCnData() of CopyNumberChromosomalModel and for
fit() of CopyNumberSegmentationModel is now
defunct.
Removed previously defunct apply() for
SampleAnnotationFile.
ROBUSTNESS: Using do.call(fcn) internally instead of
do.call("fcn").
ROBUSTNESS: Using getPathname() internally instead
of private field.
getOutputDataSet(..., onMissing = "dropall") for
AromaTransform would throw error on no applicable method
getFullNames() for NULL.apply() for SampleAnnotationFile is now defunct; use
applyTo().
Drop defunct methods.
apply() for SampleAnnotationFile to
applyTo().ROBUSTNESS: Explicitly importing core R functions.
CLEANUP: One occurance of rowMads(..., centers) to
rowMads(..., center).
CLEANUP: Drop prototype code never used.
writeRegions(..., format = "wig") gave an error.Deprecated internal whatDataType() method.
Previously deprecated methods now defunct:
nbrOfArrays() for readData() for
AromaMicroarrayDataSetTuple, AromaMicroarrayDataSet and
AromaUnitTotalCnBinarySet, as well as readData() for
SampleAnnotationFile.
Removed previously (Feb 2014) defunct method
patchPackage() and patch().
ROBUSTNESS: exportAromaUnitPscnBinarySet() asserts
that no duplicated files are returned.
getOutputDataSet() for AromaTransform gives more
informative error messages.
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.
extractRawMirroredAlleleBFractions() for
RawAlleleBFractions gave
Error in setSignals(res, dh) : object 'res' not found.
display() for Explorer would try to open a pathname in
a way that only worked on MS Windows. Thanks to Sunghee Oh (S. Korea)
for reporting on this.aromaSettings are loaded when the packages is
loaded. Previously the package had to be attached.fit2d() for matrix utilizes
use() for aroma.light.writeDataFrame(..., columnNamesPrefix="none") for
AromaUnitSignalBinaryFile would give an error.getAromaUflFile() for
AromaPlatformInterface.Move byChipType() from classes AromaCellCpgFile and
AromaCellPositionFile to superclass AromaCellTabularBinaryFile.
Package does less package reordering.
SampleAnnotationSet$loadAll() would give an error if
annotationData/samples/ didn’t exist or did not contain any
SAF files.getAromaUgpFile() for
AromaUnitSignalBinaryFile.Added SuggestsNote field to DESCRIPTION with list of
packages that are recommended for the most common use cases.
Bumped package dependencies.
ds[[idx]] instead of
getFile(ds, idx) where possible.<ns>::<fcn>() calls with repetive
<fcn>() calls; the :: operator is fairly
expensive.Previously deprecated downloadPackagePatch(),
patchPackage() and patch() for AromaPackage
are now defunct.
Removed defunct methods.
readDataFrame() for AromaGenomeTextFile and
AromaUcscGenomeTextFile explicitly passed arguments ... to
NextMethod(), which would cause them to be duplicated in
certain cases.R.rsp::rfile() for
compiling RSP files instead of the to-be-deprecated
rspToHtml().getGenericSummary() for RichDataFrame would throw
Error in data[i, , drop = FALSE] : subscript out of bounds
if it had zero rows.findChangePointsByState() for
SegmentedGenomicSignalsInterface.exportAromaUnitPscnBinarySet().onMissing to
getOutputDataSet() for AromaTransform. This replaces
argument incomplete, which will be dropped in a future
version, but is for now supported as well.Minor adjustments of NAMESPACE imports.
Updated package dependencies.
colMedians() for AromaTabularBinaryFile. If
needed, there is always colStats().Now explicitly importing only what is needed in NAMESPACE.
BACKWARD COMPATIBILITY: For R (< 3.0.2) only the maximum of 500 S3 methods are declared in NAMESPACE.
Updated package dependencies.
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.maxNAFraction when setting up the model.Now the aroma.core Package object is also available
when the package is only loaded (but not attached).
Now only importing only what is needed from the R.utils package.
Now only importing only what is needed from the matrixStats package.
ROBUSTNESS: Forgot to import
R.methodsS3::appendVarArgs().
Updated package dependencies.
Backward-compatibility code for obsolete EBImage was no longer needed.
Updated package dependencies.
exportAromaUnitPscnBinarySet() for
AromaUnitTotalCnBinarySet would throw an error on
unknown argument 'names' to indexOf().Replaced all internal x11() with
dev.new() calls.
Moved more packages from Depends to Imports.
Updated package dependencies.
findFilesTodo() for AromaTransform.Now it’s possible to call aroma.core::doCBS()
without loading package.
Turned doCBS() into a default method,
cf. aroma.affymetrix::doRMA().
help("doCBS") documents all doCBS()
methods.rm() calls with NULL
assignments.getChecksum() instead of (internal)
R.filesets::digest2() with identical results.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.CRAN POLICY: Now all Rd \usage{} lines are at most
90 characters long.
CRAN POLICY: Now all Rd example lines are at most 100 characters long.
Bumped version for CRAN submission.
No updates.
Package no longer try to apply package patches, which was only possible when namespaces where not used.
Package no longer depends on R.cache (only imports it).
is(Homo|Hetero)zygote() and
getPhysicalPositions() defunct.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")).Bumped the package dependencies.
Added an Authors@R field to DESCRIPTION.
nbrOfArrays() for AromaMicroarrayDataSet and
AromaUnitTotalCnBinarySet.No updates.
Bumped version for CRAN submission.
Utilizing new startupMessage() of
R.oo.
Bumped up package dependencies.
Now using argument colClasses (was
colClassPatterns) for all
readDataFrame():s.
getOneFile() internally.inst/reports/templates/html/archive/,
inst/reports/templates/rsp/archive/ and inst/archive/,
which all contained old/legacy Explorer versions.lapply() for AromaTabularBinaryFile to
colApply().Made several file classes implement FileCacheKeyInterface.
Added CacheKeyInterface and FileCacheKeyInterface.
getRam() and setRam() for AromaSettings
did not use memory/ram.Bumped version for CRAN submission.
No updates.
Now getParametersAsString() handles sets of
parameters as well.
Added getParameterSets() to
ParametersInterface.
Dropped getHeaderParameters() for TextUnitNamesFile,
which is now done by getHeader() of
TabularTextFile.
Package only depends on digest indirectly via R.cache.
Moved internal .assertDigest() to
R.cache.
Now using getName() instead of deprecated
getLabel().
Properly declared all cached fields, making it possible to remove
nearly all clearCache() implementations because the one for
Object takes does the job.
The RSP template for ChromosomeExplorer’s
setupExplorer.js had a duplicated entry.
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).getColumnNames() to
getDefaultColumnNames() for all classes inheriting from
GenericTabularFile, because of the new ColumnNamesInterface
interface.whichVector() with
which(), because the latter is now the fastest again.units to readDataFrame()
for AromaUnitChromosomeTabularBinaryFile.Arguments$get(Read|Writ)ablePath() instead of
filePath(..., expandLinks = "any").Added argument maxNAFraction to
CopyNumberChromosomalModel, which is now the prefer place to specify it,
instead of to fit() etc.
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".
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.Some of the HTML and CSS errors in ArrayExplorer and ChromosomeExplorer that were detected by the W3’s online validation services were correct.
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.
Object methods that calls
“next” methods, utilizes NextMethod(), which became
possible with R.oo v1.10.0.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,
trim() being overridden by ditto from the IRanges package,
iff loaded.exportAromaUnitPscnBinarySet() for a list.exportAromaUnitPscnBinarySet() for
AromaUnitTotalCnBinarySet would throw an error if the files of the
exported data set was ordered in a non-lexicographic order.downloadUGC() for AromaRepository.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.downloadCDF() for AromaRepository downloads CDFs
regardless of *.cdf and *.CDF.escape to
findAnnotationData(), which causes such symbols that exist
in argument pattern to be automatically be escaped.colBinnedSmoothing() is done over
zero-length bins, the output for those bins will be NA.colBinnedSmoothing(..., xOut = xOut) would return
binned values in the incorrect order, iff xOut was not
ordered. Added a systems test for this case.
colBinnedSmoothing(..., xOut = xOut) could generate
bins at the ends that did not contain the outer most xOut
values.
ROBUSTNESS: Now the package startup message is outputted at the very end. Previously it was done before some additional setup, which could potentially fail.
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.
Added exportAromaUnitPscnBinarySet() for
AromaUnitTotalCnBinarySet.
Added alpha versions of classes
AromaUnitPscnBinary(File|Set).
Added getNumberOfFilesAveraged() to
AromaUnitSignalBinaryFile. Formerly only for
AromaUnitTotalCnBinaryFile.
byChipType() for several annotation data file classes.calculateRatios to
CopyNumberChromosomalModel().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.
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.
CLEANUP: Package no longer “Suggests” affxparser. It was needed
because of the findFiles() function, which has been added
to R.utils v1.13.1.
Turned weightedMad() into a default method, added
help documentation with example code.
CLEANUP: Moved (internal) swapXY() and
draw() for density objects to
R.utils (>= 1.10.0).
[() for RichDataFrame would loose the class attribute,
unless argument drop was FALSE.Now colBinnedSmoothing(),
colKernelSmoothing() and
colGaussianSmoothing() returns a matrix with column names
as in argument Y.
For RawGenomicSignals, added argument fields to
binnedSmoothing() and
binnedSmoothingByField(). Also added argument
field to getSignals() and
estimateStandardDeviation().
reports/includes/js/
directory installed by ArrayExplorer and ChromosomeExplorer.Added binnedSmoothingByField() for
RawGenomicSignals.
Added subset() for RawGenomicSignals.
Added get- and setVirtualField() for
RawGenomicSignals.
Added argument sort to as.data.frame()
for RawGenomicSignals.
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.
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.
write() for RasterImage would write truncated
intensities, because we forgot to rescale [0,65535] to [0,1]
intensities.ROBUSTNESS: Added system tests for RawGenomicSignals classes.
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.
Preparing for RawGenomicSignals not being reference variables.
Preparing for supporting multiple-chromosome RawGenomicSignals.
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.
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.
x of colBinnedSmoothing() would
default to the incorrect number of loci.require.js in v2.4.4, which is needed
by the ChromosomeExplorer v3.3.setup(ce, force = TRUE)
where ce is your ChromosomeExplorer object. Thanks to Keith
Ching at ConsultChing for the initial troubleshooting
[http://consultching.com/root/?p=64] leading me on the
right track on how update ChromosomeExplorer.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.findPngDevice() uses
isPackageInstalled("Cairo") instead of
require("Cairo") to avoid loading Cairo if
not really used.findPngDevice() memoizes the results
throughout the current session.hg17 to
Human,cytobands,hg17,GLADv2.4.0,HB20100219.txt in
annotationData/genomes/Human/.drawCytoband() for ChromosomalModel failed to locate
the genome annotation data file containing cytoband information,
e.g. Human,cytobands,<tags>.txt. Thanks to Kai Wang
at Pfizer for reporting on this.base::serialize(),
because it was only applied to R (< 2.12.0) anyway and this package
now requires R (>= 2.12.0).ROBUSTNESS: Aroma settings are no longer loaded during
R CMD check.
Updated package dependencies.
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.Now colBinnedSmoothing() handles an unordered
xOut.
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.
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.
Added plotCoverageMap() for AromaUgpFile.
getDefaultExtension() for
UnitAnnotationDataFile, which guesses the filename extension from the
class name, unless overridden by a subclass.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.
CLEANUP: Now getFullNames() for
AromaMicroarrayDataSetTuple no longer produces a warning on
is.na() applied to non-(list or vector) of type 'NULL'.
exportTotalCnRatioSet() for AromaUnitTotalCnBinarySet
and exportFracBDiffSet() for AromaUnitTotalCnBinarySet
tried to call cat(verbose, x) with
length(x) > 1.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.extractPSCNArray() for
AromaUnitTotalCnBinary{File|Set}.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.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.cat() and getOption() of
R.utils (instead of ‘base’).getSnpNucleotides() for AromaCellSequenceFile.hpaste() internally wherever
applicable.allocateFromUnitAnnotationDataFile() for
AromaUnitTabularBinaryFile would include chip type tags in the path,
e.g. annotationData/chipTypes/GenomeWidesSNP_6,Full.Now ChromosomeExplorer does a better job of listing chromosomes that are specific to the genome/organism used.
Added getChromosomeLabels() for
ChromosomeExplorer.
lapplyInChunks(idxs) for numeric did not correctly
handle the case when length(idxs) == 0, because of a
typo.Updated the default filename patterns used by
findByGenome() for AromaGenomeTextFile to
"^%s,chromosomes(|,.*)*[.]txt$".
GENERALIZATION: Now findByGenome() for
AromaGenomeTextFile follows the new aroma search conventions.
GENERALIZATION: In addition to search
<rootPath>/<set>/<name> paths,
findAnnotationData() can also search
<rootPath>/<set>/ 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.
Now getGenomeFile() for ChromosomalModel utilizes
byGenome() for AromaGenomeTextFile to locate the genome
annotation file.
Added static loadAll() for
SampleAnnotationSet.
getUnitsOnChromosomes() for
AromaUnitChromosomeTabularBinaryFile truly returns valid
unit indices. Thanks to Emilie Sohier, France for reporting
on a problem related to this.STANDARDIZATION: Now the default output path for all
allocateFromUnitAnnotationDataFile() is
annotationData/chipTypes/<chipType>/. 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.
GENERALIZATION: getAverageFile() for
AromaUnitTotalCnBinarySet first searches for an existing result file
according to the new search conventions. If not found, then it’s
created.
GENERALIZATION: Now the default for createImage()
for matrix is to test to create images according to aroma settings
option output/ImageClasses.
ROBUSTNESS: Now getAverageFile() for
AromaUnitTotalCnBinarySet creates the result file atomically by writing
to a temporary file which is renamed afterward.
Now write() and read() for RasterImage
throws an informative error message explaining that the
png package is needed.
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.
colorize() for Image tried to call
createImage() using a vector instead of a matrix.
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.
findAnnotationData() to be annotationData/ and
annotationData,<tags>/.getTags() to Arguments to
R.filesets v0.9.3.Deprecated static method importFromTable() for
FileMatrix.
Removed several deprecated methods.
Submitted to CRAN.
No updates.
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.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).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. MS Windows 7 64-bit.
Added alpha version of an internal RasterImage class.
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.Deprecated internal as.TrueColorImage() for Image
and for matrices.
Removed deprecated internal rgbTransform() for
Image.
digest() uses the faster
serialize() of R v2.12.0. The earlier version was orders of
magnitude slower on MS 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.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").Mouse,chromosomes.txt to
system.file("annotationData/genomes/Mouse", package = "aroma.core").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.
Added requireWithMemory().
plot() for CopyNumberSegmentationModel would throw
exception
Cannot infer number of bases in chromosome. No such chromosome: 25
for chromosome 25.
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.
ROBUSTNESS: Now subsample() for BinnedScatter
utilizes resample().
CLEANUP: Removed stext(). It is in
R.utils.
CLEANUP: Removed some outdated patches for R v2.7.0 and before.
CLEANUP: Package no longer need to “suggest” geneplotter.
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).
Now optional arguments ... to
CopyNumberChromosomalModel are recorded.
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.Added drawDensity() for CopyNumberRegions and
RawGenomicSignals.
Added getDensity() for CopyNumberRegions which
returns the empirical density of the mean levels weighted by the region
lengths.
Added getLength() for CopyNumberRegions, which
returns a vector of region lengths.
Now the ylim defaults to c(0,5) for
plot() for RawCopyNumbers.
Added basic support for operators +, -,
and * to RawGenomicSignals.
Added the AromaGenomeTextFile class.
Added genome annotation file
Canine,chromosomes,UGP,HB20100822.txt to
system.file("annotationData/genomes/Canine", package = "aroma.core").
annotationData/genomes/Human/Human,chromosomes.txt had
an extra TAB on the ChrM row.Added abstract classes SegmentationDataFile and
SegmentationDataSet to represent segmentation data results. Current
subclasses are CbsSegmentationData(File|Set).
Added more utility methods for CopyNumberRegions.
xRange(), prune(),
simulateRawCopyNumbers(), +(),
-() and *().writeDataFrame() for AromaUnitTotalCnBinarySet
and AromaUnitFracBCnBinarySet to get the correct filename extension.
Thanks Nicolas Vergne at the Curie Institute for reporting this.Added subset() for CopyNumberRegions.
Now extractRegion() for RawGenomicSignals also
accepts a CopyNumberRegions object for argument
regions.
Added extractRegions() for
RawGenomicSignals.
writeDateFrame() for AromaUnitSignalBinarySet would
write the same data chunk over and over.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.as.GrayscaleImage(..., transforms = NULL) for
matrix would throw
Exception: Argument transforms contains a non-function: NULL.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.Added trial version of fullname translator files.
doCBS() for character:s support data set
tuples.
Added doCBS() for CopyNumberDataSetTuple:s.
R CMD check on R v2.11.0 and v2.12.0
devel.path of all writeDataFrame()
methods defaults to
<rootPath>,txt/<dataSet>/<chipType>/.Added writeDataFrame() for
AromaUnitTabularBinaryFile.
Added argument columnNamesPrefix to all
writeDataFrame().
AD HOC: Now getUnitAnnotationDataFile() of
AromaPlatformInterface load aroma.affymetrix if needed
and if installed.
writeDataFrame() for
AromaUnitSignalBinary{File|Set}.getFitFunction() of CbsModel would return a function
that would give
Error in segmentByCBS.RawGenomicSignals(..., seed = seed): formal argument "seed" matched by multiple actual arguments.Added equals() for CopyNumberRegions.
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.
seed to segmentByCBS() for
RawGenomicSignals.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.
Now segmentByMPCBS() can be used to segment data
from a single source.
segmentByMPCBS() for RawGenomicSignals.verbose of getOutputSet()
of ChromosomalModel.Submitted to CRAN.
No changes since v1.4.7.
Package passes R CMD check on R v2.10.1 patch and R
v2.11.0 devel.
Package passes all redundancy tests.
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.
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).
Added Human cytoband files to
annotationData/genomes/.
Added annotationData/genomes/ to
aroma.core (from
aroma.affymetrix).
Added getOutputSet() for ChromosomalModel.
Added alpha version of a doCBS().
SIMPLIFICATION: Now it is possible to use ChromosomeExplorer without having to install the GLAD package (used before for cytobands).
SIMPLIFICATION: Now it is possible to plot cytobands without having to install the GLAD package.
print() statements in
isCompatibleWith().R CMD check and all redundancy
tests.getChromosomes() for
class AromaUnitChromosomeTabularBinaryFile validating that the file has
a chromosome column.Arguments$getTags() where ever
possible.ChromosomalModel:s (and and the ChromosomeExplorer) no longer require unit names files.
getListOfAromaUgpFiles() for ChromosomalModel no
longer goes via getListOfUnitNamesFiles(). This opens up
the possibility to work with data files without unit names files,
e.g. smoothed CN data.
Added getAromaUgpFile() for
AromaPlatformInterface.
getUnitNamesFile() for AromaPlatformInterface
utilizes the generic getUnitAnnotationDataFile()
method.defaults to allocate() of
AromaTabularBinaryFile.segmentByMPCBS() via the
mpcbs package.R CMD check on R v2.10.1 and R v2.11.0
devel and all of its redundancy tests.getDefaultFullName() for AromaMicroarrayDataSet
and AromaTabularBinarySet in order to override (parent = 1)
the new default of GenericDataFileSet in R.filesets
v0.7.0, which would return the chip type (parent = 0) as
the name.getPairedNames() to CopyNumberChromosomalModel
which returns combined <test>vs<ref> names,
e.g. TumorvsNormal. The default behavior is that if
<ref> is the average of a pool, then the paired name
is <test>, e.g. Tumor.Added argument pattern to byName() for
AromaUnitTotalCnBinarySet and AromaUnitFracBCnBinarySet.
getSets() of AromaMicroarrayDataSetTuple overrides
the default method by adding the chip types as the names of the returns
list.
ROBUSTNESS: Using new Arguments$getInstanceOf() were
possible.
ROBUSTNESS: Now CopyNumberChromosomalModel() asserts
that none of the test samples have duplicated names.
ROBUSTNESS: Now all index arguments are validated correctly using
the new max argument of
Arguments$getIndices(). Before the case where
max == 0 was not handled correctly.
getSetTuple() from
ChromosomeExplorer.translateFullNames() of ChromosomeExplorer would
translate the full names, but return the original ones.
getFullNames() of ChromosomeExplorer reported:
Error in UseMethod("translateFullNames"): no applicable method for translateFullNames applied to an object of class "character".
extractMatrix() of AromaUnitCallFile did not recognize
NoCalls.extractRawCopyNumbers() for RawCopyNumbers would give
an error if the internal logBase was NULL.xScale = 1e-6 by
default.Added extractRawCopyNumbers(, ...logBase = 2) to
RawCopyNumbers, which can be used to change the logarithmic base of CN
ratios, if any.
Added getAverageFile() for
AromaUnitTotalCnBinarySet.
Moved ChromosomeExplorer to aroma.core from aroma.affymetrix.
Moved several method for profileCGH objects to
aroma.core from
aroma.affymetrix.
ALPHA: First successful run of segmentation with CbsModel with AromaUnitTotalCnBinarySet data sets.
Added isAverageFile() for
AromaUnitSignalBinaryFile.
Added class AromaUnitTotalCnBinarySetTuple.
Added interfaces CopyNumberDataFile, CopyNumberDataSet, and CopyNumberDataSetTuple (internal for now).
GENERALIZATION: Moved CbsModel, GladModel and HaarSegModel (all segmentation models) of aroma.affymetrix to here.
GENERALIZATION: Moved all (generalized) ChromosomalModel, CopyNumberChromosomalModel, and CopyNumberSegmentationModel from aroma.affymetrix to here.
getAromaUflFile() to UnitAnnotationDataFile.Now AromaUflFile$allocateFromUnitNamesFile()
works.
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.
New public release.
More recent dependencies on Bioconductor packages.
R CMD check on R v2.10.0 and all
redundancy tests.getExtensionPattern() to most GenericDataFile
classes.setName() for RawGenomicSignals.CLEANUP: Updated to use byPath() instead
fromFiles().
CLEANUP: Move the Interface class to the R.oo package.
R CMD check on R v2.9.2 and all
redundancy tests.getUnitsOnChromosomes() for
AromaUnitChromosomeTabularBinaryFile returns a vector by default
(unlist = TRUE).Added yRange(), yMin() and
yMax() for RawGenomicSignals.
Added extractRawCopyNumbers() for
RawSequenceReads.
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.totalAndFracBData/ to the search path of
byName() for AromaUnit(FracB|Total)CnBinarySet.Added allocateFromUnitAnnotationDataFile() for
AromaUnitSignalBinaryFile and AromaUnitTabularBinaryFile.
Added getUnitTypesFile() for AromaPlatform and
AromaPlatformInterface.
Added UnitAnnotationDataFile, which now the UnitNamesFile and the new UnitTypesFile inherits from.
Now uses() for Interface takes multiple
Interface:s.
Added class RawSequenceReads.
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.
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.
Added get-, setStateColorMap(), and
getStateColors() for class
SegmentedGenomicSignalsInterface.
Added argument keepUnits = FALSE to
extractRawGenomicSignals() of
AromaUnitSignalBinaryFile.
Now RawGenomicSignals(y = rgs) sets all locus fields
in rgs if it is a RawGenomicSignals object.
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.exportTotalCnRatioSet() would return a
AromaUnitFracBCnBinarySet.is(Homo|Hetero)zygous(), not
is(Homo|Hetero)zygote().ADDED: Added support for “birdseed” encoding in
extractGenotypes() and updateGenotypes() of
AromaUnitGenotypeCallFile.
Added SegmentedGenomicSignalsInterface, which implements all the methods for SegmentedCopyNumbers and the new SegmentedAlleleBFractions.
Added getFields() to Interface as an ad-hoc
solutions to avoid print(<Interface>) throwing
Error in UseMethod("getFields") : no applicable method for "getFields".
updateGenotypes() of AromaUnitGenotypeCallFile
is now much faster in counting A:s and B:s.isHomozygote() of AromaUnitGenotypeCallFile was not
correct.
getOutputDataSet() of AromaTransform failed to
identify the output files if (and only if) a filename translator was
applied to the input data set.
New public release.
No updates.
R CMD check on R v2.9.0 and all
redundancy tests.Added extractRawAlleleBFractions() for
AromaUnitFracBCnBinaryFile.
Added exportFracBDiffSet() for
AromaUnitFracBCnBinarySet.
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.
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.
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.
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.
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.
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.Moved the Explorer class and its support files under
inst/ from aroma.affymetrix to
aroma.core.
Moved the AromaCellPositionFile class from aroma.affymetrix to aroma.core.
CLEANUP: Moved all file set specific classes and methods to the new R.filesets package.
allocateFromUnitNamesFile() for
AromaUnitSignalBinaryFile would not call generic allocate()
but the one for this class.
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.
binnedSmoothing() of RawGenomicSignals uses
weighted estimates (by default) if weights exists.Added RawAlleleBFractions() extending
RawGenomicSignals.
Added extractCopyNumberRegions() for profileCGH,
DNAcopy, and HaarSeg segmentation object. Before they were in
aroma.affymetrix.
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.
Added extractRegion() to RawGenomicSignals.
Added getWeights() and hasWeights() to
RawGenomicSignals.
Added {add,subtract,multiply,divide}By() for
RawGenomicSignals all utilizing support method
applyBinaryOperator().
ALPHA: Added classes GenericDataFile{Set}List.
ALPHA: Added class AromaUnitTotalCnBinaryFileList with methods
extractRawCopyNumbers() and
extractMergedRawCopyNumbers().
Now aroma.core works with the IRanges and grid packages, regardless on the order they were loaded.
getPlatform() of TextUnitNamesFile would sometimes
return a list of length one, instead of an single character
string.
extractSubset() of RawGenomicSignals did not
recognize all locus fields.
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.
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.
UPDATE: Replace argument robust of
colBinnedSmoothing() with a more generic FUN
argument. The default arguments give identical results.
Now static fromFiles() of GenericDataFileSet
supports empty data sets.
Now readDataFrame() of AromaUgpFile and
AromaUnitTabularBinaryFile accepts
rows = integer(0).
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.
Added extractByChromosomes() for
AromaUgpFile.
Added argument translate to
getColumnNames() of TabularTextFile.
R CMD check on R v2.9.0.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.
lines() of RawGenomicSignals did not recognize
xScale and yScale.
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).
as.character() of GenericDataFileSet would throw an
error if the data set was empty, because then there was no
path.
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.
binnedSmoothing(..., byCount = TRUE) of
RawGenomicSignals would give error
[...] object "ys" not found.
When passing a single data points to
colBinnedSmoothing(), it would throw the exception:
Range of argument 'by' is out of range [0,0]: [<by>,<by>].
Added argument units to
extractRawCopyNumbers() of
AromaUnitSignalBinaryFile.
Added RawGenomicSignals which RawCopyNumbers now inherits from.
Added readDataFrame(..., units = NULL) to
AromaUnitSignalBinaryFile.
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.
Added hasBeenModified() to GenericDataFile.
Now hasTags(..., tags) of GenericData{File|Set}
splits the tags argument.
Now RawCopyNumbers() takes RawCopyNumbers objects as
input.
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.
getChecksum() of GenericDataFile caches results
unless the file has been modified since last time.byName() of AromaUnit(FracB|Total)CnBinarySet
searches rawCnData/ then cnData/.Added SegmentedCopyNumbers class.
Added various smoothing methods to RawCopyNumbers.
Added colBinnedSmoothing() and
colKernelSmoothing().
Added getAromaUgpFile() to UnitNamesFile.
Added shakyText().
Added static byChipType() to UnitNamesFile.
Added argument fullname to
getChipType() of AromaUnitSignalBinaryFile.
Now argument files in extract() of
GenericDataFileSet can also be a vector of string.
ALPHA: Added support for “smart” (e.g. "*")
subdirectories in static findByName() of
GenericDataFileSet.
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.
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.
ROBUSTNESS: Now findAnnotationData() always returns
pathnames ordered by the length of their fullnames. Before this was only
done if firstOnly = TRUE.
Added getMaxLengthRepeats() to
AromaCellSequenceFile.
Added AromaUnitSignalBinary{File|Set}, AromaUnitTotalCnBinary{File|Set}, AromaUnitFracBCnFinary{File|Set}, AromaUnitCall{File|Set}, and AromaUnitGenotypeCall{File|Set}.
readFooter() of AromaTabularBinaryFile did not
return the correct list for nested structures.
groupBySnpNucleotides() of AromaCellSequenceFile
would return an empty element missing for some chip types,
e.g. Mapping10K_Xba142. Now such empty elements are dropped.
getAttributes() for GenericDataFile:s would give an
error if there were no attributes.
SPEEDUP: Now predict() of ProbePositionEffects is
6-7 times faster.
SPEEDUP: Now the result of isMissing() for
AromaCellSequenceFile can be cached.
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.R CMD check on R v2.7.2 and R
v2.8.0rc.as.GrayscaleImage()
in argument transforms to a list using
as.list() and not list().skip to writeChecksum() of
GenericDataFile.getSnpPositions(), getSnpShifts(),
getSnpNucleotides(), and
groupBySnpNucleotides() to AromaCellSequenceFile.fitGenotypeCone() to support both flavors
"sfit" (old) and "expectile" (new).Added support for argument positions to
countBases() for AromaCellSequenceFile.
ALPHA: Added fitMultiDimensionalCone().
readSequences() for AromaCellSequenceFile translated
raw values to incorrect nucleotides.R CMD check on R v2.7.1 and R v2.8.0
devel on MS Windows XP.getCreatedOn(), getLastModifiedOn(),
and getLastAccessedOn() to GenericDataFile. These a just
wrapper accessing file.info() fields.SPEEDUP: Added patch for base::serialize() on MS
Windows, which in turn will speed up digest::digest() and
all methods that use the latter to generate hashcodes.
SPEEDUP: 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.
SPEEDUP: Replaced all which() with faster
whichVector().
updateDataColumn() coerce values to doubles before
censoring them for raw and integer columns.Now countBases() of AromaCellSequenceFile returns
“raw” counts if argument mode = "raw".
ALPHA: Added setFullName() and
setName() to GenericDataFile and GenericDataFileSet. The
plan is to have these replace what getAlias() and
setAlias() do today.
BETA: Added setFullNameTranslator() to
GenericDataFileSet.
findByName() assert that the data set name is not
empty.BETA: Added setFullNamesTranslator() (for the files)
to AromaGenericFileSet.
ALPHA: Added protected update2() to
GenericDataFileSet.
ALPHA: Added private ProbePositionEffects, etc.
Added a general importFrom() for
AromaTabularBinaryFile, which calls matching
importFrom<ClassName>(), if found.
Added support for raw data columns in
AromaTabularBinaryFile.
BETA: Added readTableHeader().
BETA: Added AromaCellSequenceFile.
BETA: Added classes AromaMicroarrayTabularBinaryFile and AromaCellTabularBinaryFile.
readDataFrame():
R CMD check on R v2.7.0 patched.getOutputFiles() of
AromaTransform.Added AromaTransform (extracted from
aroma.affymetrix::Transform).
Added nbrOfArrays() to
AromaMicroarrayDataSet.
Now private xmlToList() handles more complex XML
strings.
Added member chromosome to RawCopyNumbers.
Added gaussianSmoothing() to
RawCopyNumbers.
Added argument xOut to
gaussianSmoothing() in order to specify at what loci the
smoothed signals should be calculated.
Added gzip()/gunzip() to
GenericDataFile.
Added static findByName() and byName()
to GenericDataFileSet.
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.
Added validate() to GenericDataFileSet, which is
called at the end of
fromFiles(..., .validate = TRUE).
Added extractMatrix to GenericTabular(File|Set) and
AromaTabularBinary(File|Set).
Added equals() and hasFile() to
GenericDataFileSet.
Added classes GenericTabularFileSet and AromaTabularBinarySet.
Added stextChipType() for strings.
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.
ALPHA: Added full name translation for GenericDataFile:s.
ALPHA: Added UnitNamesFile.
Package passes R CMD check on R v2.7.0
patched.
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().
stextNnn() methods from AffymetrixFile to
AffymetrixMicroarrayDataSet. Created superclass
AromaMicroarrayDataSetTuple of AffymetrixCelSetTuple.BUG FIX: readDataFrame() did not read the first data
row if there was no column header; it was eaten up by a preceeding
readHeader().
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.
Package created.
Took all core classes and core methods in aroma.affymetrix that are independent of the Affymetrix platform and placed the here.
The version is numbered starting from the current version of aroma.affymetrix.
interleave() for Image gave
Error in z[idxOdd, ] : incorrect number of dimensions.
The internal image structure is a 3-dim array.
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.