January 2007 affxparser Added convertCel() and compareCels() Added argument 'writeMap' to updateCel() Bugfix: Using argument 'readMap' in readCel() would give an error Now readCdfUnits(..., readDirections = TRUE) also returns unit group directions Added cdfAddPlasqTypes() Now readCdf() reads all unit and group fields by default Read maps can be used to unrotate CEL data rotated by dChip software Added writeCdfHeader(), writeCdfQcUnits() and writeCdfUnits(). These are all used by writeCdf(), and make it possible to write a CDF in chunks in order to, for instance, convertCdf() using constant memory affy Added checkValidFilenames() to ensure that what is passed to e.g., ReadAffy() are actually celfiles, and give a reasonable warning if not affycoretools Bug fixes to vennSelectBM(). Added code to remove illegal filename characters, and corrected subsetting of exprs matrix to result in a matrix even if it is only one row affyPLM PLMset objects no longer have direct dependence on eSet objects (nor exprSets as done historically). Removed all exprSet functions or replaced with ExpressionSet equivalents annaffy Added compatibility for SQLite-based annotation data packages. This patch allows annaffy to be used with environment and SQLite-based annotation packages. The vignette has been converted to use the hgu95av2db package for testing purposes annotate Import AnnotationDbi, fixed lookUp() to work with SQLite-based packages. With these changes you can load SQLite-based packages such as hgu95av2db and use lookUp() with it (you still specify "hgu95av2", not "hgu95av2db") annotationTools New Package: Functions to annotate microarrays and mine for orthologs from flat file databases (plain text files). Maintainer: Alexandre Kuhn aroma.light Bug fix: averageQuantile.list() would not accept vector of different lengths. Thanks Alicia Oshlack Biobase Fixed code in openVignette() to give a better error message when the installed package doesn't contain a PDF vignette Provided a more detailed example for read.AnnotatedDataFrame() Clarified ExpressionSet documentation biomaRt Fixed bug in getBM() when output is a list Added getLDS() (linked data set) function which enables one to link two BioMart datasets and construct a combined query of both datasets (e.g., in homology mapping) Category Fixed show() method to work on all HyperGParams objects instead of just GOHyperGParams objects Changed vignette and man pages to use hgu95av2db cghMCR Bug fix that allows the code to exit gracefully when failing to detect any altered segments copa Added summaryCopa() to ouput a data.frame of genes that have a certain number (or greater) of outliers Fixed some errors in the vignette cosmo GUI for interactively constructing constraing sets has been moved into separate package cosmoGUI Functions for plotting DNA sequence logos have been moved in to separate package seqLogo Added 'maxIntensity' parameter to cosmo() to allow likelihood to be maximized wrt to intensity parameter as well Default value for 'intCrit' changed from 'eval' to 'lik' simScoree() now takes argument 'minOverlap' specifying minimal overlap between predicted and true motifs to declare a hit Relaxed checks on starting values for satisfying constraints to avoid not finding any starting values Uninitialized starting falues are now skipped Fixed bug in computing E-value for sequences wtih unknown characters fixed A number of default options have been changed on the basis of new simulation results: wCrit changed from 'eval' to 'bic' modCrit changed from 'eval' to 'lik' conCrit changed from 'pwmCV' to 'likCV' conTrunc changed from 100 to 90 cosmo() now accepts a file for specifying the background Markov model that follows the MEME standard New function bfile2tmat() converts a MEME-style background file into a transition matrix New function bgModel() produces an estimate of the transition matrix for the background Markov model A useful error message is printed if input sequence file or background sequence file contains a sequence of length zero cosmoGUI New Package: cosmoGUI allows the user to interactively define constraint sets that can be used by the cosmo package to supervise the search for shared motifs in a set of DNA sequences. The constraints can be either adapted from a set of commonly used templates or defined from scratch. Maintainer: Oliver Bembom DynDoc Fixed Vignette class definition. The Vignette class was using a non-existent VersionNumber class for one of its slots. For now, we'll use the version number class defined in base as s3 'package_version' Fixed show() methods for SweaveOptions(), codeChunk(), and chunkList() exonmap New Package: Provides high level functions for reading Affy .CEL files, phenotypic data, and then computing simple things with it, such as fold-changes t-test and so on. Applies fine grained genome-wide annotation to the data. Maintainer: Michal Okoniewski genefilter Added AnnotationDbi to genefilter imports. This is required to integrate SQLite-based annotation data packages. By importing, we get the AnnotationDbi defined environment API functions such as mget() to do the right thing when the data map is an S4 class instead of an environment GeneticsDesign New Package: This package contains functions useful for designing genetics studies, including power and sample-size calculations. Maintainer: Weiliang Qiu GOstats Improved plotTermGraphs(). Use GO term names in the plot insead of GO IDs. This can be toggled using use.terms, but default is TRUE. We also show x/y for each node, which is the number from the selected list over the number in the category Changed the default for summary(GOHyperGResult) to use htmlLinks=FALSE at the command line for readability Refactored result plotting. Return graph objects instead of each helper function producing a plot. Then a single plot helper function plotGOTermGraph() can be used to produce a nicely labeled plot Fixed coloring of plotGOTermGraph() to shade only significant nodes. Nodes for which we did not test are labeled with 0/?. Colors can be specified graph Improvements to vignette Moved edgeL-method for distGraph and clusterGraph from Rgraphviz to graph LBE New Package: LBE is an efficient procedure for estimating the proportion of true null hypotheses, the false discovery rate (and so the q-values) in the framework of estimating procedures based on the marginal distribution of the p-values without assumption for the alternative hypothesis. Maintainer: Cyril Dalmasso limma Old functions designed to read image data files into data.frames are now deprecated. This affects read.matrix(), rg.series.spot(), read.series(), m.spot(), a.spot(), rg.spot(), rg.quantarray(), rg.genepix() wtVariables() renamed to namesInFun() New argument 'other.columns' for read.imagene() User's guide sections on spot quality weights and quality assessment expanded normalizeForPrintorder(plot=TRUE) now produces no output to agree with the documentation lumi New Package: lumi R package is designed to preprocess the Illumina microarray data. It includes functions of Illumina data input, quality control, variance stabilization, normalization and gene annotation. Maintainer: Pan Du rHVDM New Package: A R implementation of HVDM (Genome Biol 2006, V7(3) R25) Maintainer: Martino Barenco seqLogo New Package: seqLogo takes the position weight matrix of a DNA sequence motif and plots the corresponding sequence logo as introduced by Schneider and Stephens (1990). Maintainer: Oliver Bembom SLqPCR New Package: Functions for analysis of real-time quantitative PCR data at SIRS-Lab GmbH Maintainer: Dr. Matthias Kohl topGO New Package: topGO package provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be implemented and applied. Maintainer: Adrian Alexa vsn Added a function for visualization of the loglikelihood Added functions for reference normalization ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
[Bioc-devel] NEWS
1 message · James W. MacDonald