February 2007 ABarray Modified to use ExpressionSet instead of exprSet affxparser Now readCelunits() can handle unit groups for which there are no probes, e.g., when stratifying on PM in a unit containing only MMs. Added writeCdfHeader(), writeCdfQcUnits() and writeCdfUnits(), all of which are used by writeCdf(). They make it possible to write a CDF in chunks using bounded memory. annaffy Updated AmiGO URL beadarray Changed structure of class BeadLevelList to handle uneven numbers of beads per array, and two-colour data. Updated plotting and summarising functions. Added boxplotBeads(), arrayNames(), numBeads(), getArrayData() to work on this class. New function readIllumina() to read in raw bead-level data. Biobase Added experimental unsaveSetSlot for internal use. This functiona llows one to set the slots of an S4 object in place without any copying. This should allow for considerable speed up when used appropriately. Added ExpressionSet introduction vignette. Moved old Biobase vignette to new 'legacy' directory. Disallowed drop = TRUE for AnnotatedDataFrame. biomaRt Added port attribute to listMarts() and useMart() so users can choose which port to connect to when using biomaRt in MySQL mode. Changed default Ensembl host to martdb.ensembl.org using port 3316. Added retrieval of more sequence types with the getSequence function (such as retrieval of exons and upstream sequences). One can now also use filters for the type argument of getSequence(). Removed getXref() and getPossibleXrefs() as these have been deprecated by getBM() and getLDS(). Removed the martTable object as ouput from all functions is now a data.frame. Biostrings Added the Boyer-Moore algorithm. The defaults for matchPattern() are now fixed = TRUE and the 'auto' feature ow picks up the 'boyer-moore' algorithm whenever possible (generally faster than the shift-or algorithm. Added the 'naive' algorithm for QC and as a benchmark. Added the 'gregexpr' algorithm when pattern and subject are both standard character strings. The 'gregexpr' algorithm is a modified version of the standard R gregexpr(), to be used as a 'pure R' benchmark. Changed modified gregexpr() to gregexpr2() and added gregexpr(). Both undocumented. Terminology changes. The 'Strong Good Suffix shifts' are now called the 'Very Strong Good Suffix shifts' to indicate the difference (>=) from the usual Strong Good Suffix shifts. The 'Good Right Shifts' are now called the 'Matching Window shifts'. Category Added ability to run huperGTest() using chromosome bands as categories. This adds the ChrMapHyperGParams and ChrMapHyperGResult classes and code. Improved handling of MAP annotation ranges. Instead of dropping annotations given as a range of chromosome bands, we now take the longest common prefix. There are still some inconsistencies in the annotation which we don't handle perfectly. Removed unused geneCounts and universeCounts from HyperGResult object. Methods with the same names are available for accessing these data from the result object. Thanks to N. Le Meur for the bug report. cellHTS Added two new summaries that can be used in summarizeReplicates(), 'closestToZero' and 'farthestFromZero'. EBImage Bug fix: memory of the size of unpacked image was lost on every operation using ImageMagick built in filters. Other filters were not affected, nor were IO, conversions or object detection. Everyone using the package should update to this version. Added propagate(), a Voronoi-based segmentation on image manifolds with modified metric. exonmap gene.details(), transcript.details() and exon.details() now take a vector as input and return a data.frame (as advertised). pc() now uses rowttests(), and does not need members to be specified if factor has exactly two levels. Added gene.strip() and probesets.in.eset(). Improved scale on plot.gene(). gcrma Changed optical background correction to tolerate no MM arrays. graph Added edgeMatrix method for graphAM. Fixed graphNEL ==> graphAM by removing rownames from adjMat. The optimized version was resulting in a graphAM instance with rownames and colnames on the adjMat. The graphAM initialize method removes rownames so the node names are stored once. Fixed bug in ftM2graphNEL() that was due to partial string matching in accessing list elements by name. limma normalizeRobustSpline() now works with only one print-tip group. New function mergeScahsRG(). Deprecated getColClasses() and namesInFun() and replaced with read.columns(), a more general function that is similar to read.delim() but reads specified columns only. Argument '...' added to all as.matrix methods for compatibility with R-2.5.0. Bugfix: lm.series() and gls.series() were returning errors when the design matrix was not of full rank and the columns were names. Bugfix: write.fit() was using ambiguous column names for the coef, t-statistic and p-value when the MArrayLM object had only one column and these components were matrices with one named column. Default for digits changed in write.fit(). lumi Updated lumiR() to allow directly adding nuID when reading the data, and updated addNuId2lumi to add the tracking history. Updated the combine method of LumiBatch class, addNuId2lumi(), lumiR() for better adaptiveness. pcaMethods Added support for non-linear PCA and made corresponding additions to the documentation. Also added simulated example data for use with nlpca(). Changed Q2 cross-validation to guarantee that no full column or row is ever deleted. The screeplot() function was removed and replaced with plotR2(). K-estimate now supports NMRMSEP and Q2 as error measure. Upgraded plotPcs() so it works with Sweave() and gives prettier output by basing it on pairs() instead of slplot(). Added a new method kEstimateFast(). This also estimates the best number of components/similar genes for missing value estimation. In contrast to kEstimate() no crossvalidation is performed. This is a more rough estimate than provided by kEstimate(). Improved speed of kEstimate(). Now possible to get the estimation error for each individual incomplete variable. This allows one to easily see for which variables missing value imputation makes sense. Removed ellipse dependency. Added vignette on missing value estimation. New method to comvert pcaRes to exprSet. pca() no longer returns an exprSet if an exprSet was used as input, use asExprSet() instead. simpleaffy Added C. elegans and yeast2 to data for QC stats. Updated to work with ExpressionSet class. vsn Improvements on the predict method for vsn(). justvsn() is now exported. Updated lymphoma dataset to ExpressionSet. Made vsn2() compatible with limma package. Updated vignette. ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
[Bioc-devel] February NEWS
1 message · James W. MacDonald