[Bioc-devel] NEWS

James MacDonald jmacdon at med.umich.edu
Mon Feb 5 17:13:02 CET 2007

	January 2007

	Added convertCel() and compareCels()
	Added argument 'writeMap' to updateCel()
	Bugfix: Using argument 'readMap' in readCel() would give an
	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
	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

	Added checkValidFilenames() to ensure that what is passed to
	e.g., ReadAffy() are actually celfiles, and give a reasonable
	warning if not

	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

	PLMset objects no longer have direct dependence on eSet
	objects (nor exprSets as done historically). Removed all
	exprSet functions or replaced with ExpressionSet equivalents

	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

	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")

	New Package:
		Functions to annotate microarrays and mine for
		orthologs from flat file databases (plain text files).
		Alexandre Kuhn

	Bug fix: averageQuantile.list() would not accept vector of
	different lengths. Thanks Alicia Oshlack

	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
	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)

	Fixed show() method to work on all HyperGParams objects
	instead of just GOHyperGParams objects
	Changed vignette and man pages to use hgu95av2db

	Bug fix that allows the code to exit gracefully when failing
	to detect any altered segments

	Added summaryCopa() to ouput a data.frame of genes that have a
	certain number (or greater) of outliers
	Fixed some errors in the vignette

	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

	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
		Oliver Bembom

	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
	Fixed show() methods for SweaveOptions(), codeChunk(), and
	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

		Michal Okoniewski

	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

	New Package:
		This package contains functions useful for designing
		genetics studies, including power and sample-size
		Weiliang Qiu

	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

	Improvements to vignette
	Moved edgeL-method for distGraph and clusterGraph from
	Rgraphviz to graph

	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.
		Cyril Dalmasso

	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
	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.
		Pan Du		

	New Package:
		A R implementation of HVDM (Genome Biol 2006, V7(3)
		Martino Barenco

	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).
		Oliver Bembom

	New Package:
		Functions for analysis of real-time quantitative PCR
		data at SIRS-Lab GmbH
		Dr. Matthias Kohl

	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.
		Adrian Alexa

	Added a function for visualization of the loglikelihood
	Added functions for reference normalization

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