[Bioc-devel] NEWS March 2007

James MacDonald jmacdon at med.umich.edu
Wed Apr 4 16:55:15 CEST 2007

	March 2007

	New Package:

	    ACME (Algorithms for Calculating Microarray Enrichment) is
	    a set of tools for analysing tiling array ChIP/chip, DNAse
	    hypersensitivity, or other experiments that result in
	    regions of the genome showing "enrichment".  It does not
	    rely on a specific array technology (although the array
	    should be a "tiling" array), is very general (can be
	    applied in experiments resulting in regions of
	    enrichment), and is very insensitive to array noise or
	    normalization methods.  It is also very fast and can be
	    applied on whole-genome tiling array experiments quite
	    easily if enough memory is present.


		Sean Davis


	Added argument 'truncateGroupNames' to readCdfGroupNames()
	which defaults to TRUE. When TRUE, any prefix of group names
	identical to the unit name will be stripped of the group


	updateObject() now removes empty or inconsistent se.exprs from
	AffyBatch objects

	Return new('matrix') rather than NULL if se.exprs undefined

	Updated GO url, fixed bug in getGOUrl()


	Added getAnnMap() and annPkgName(). getAnnMap() provides a
	single interface for retrieving map objects from both SQLite
	and environment-based annotation data packages. AnnPkgName()
	is a simple helper that returns the package name given chip
	and package type (db or env)

	Add aqListGOIDs() to list GO IDs in specified ontologies
	Changed default behavior of getAnnMap(). The default value of
	load is now TRUE. If type is missing then we use the first
	matching package on the search path and only then fall back to
	loading based on the default value for type


	Added the AnnObject and AnnTable classes. The AnnMap class
	(and its subclasses) now derive from the AnnObject class

	Added an as.data.frame() method for AnnTable objects
	Added the RawAnnMap class and use it in the AFFYHUEX_DB schema

	Added as.list() for RawAnnMap objects

	Added new generics toTable() and toList() as replacements for
	as.data.frame() and as.list()


	Bugfix to qcBeadLevel() and new arg experimentName for HTML
	report heading


	Enabled display of attribute/filter groups and categories. A
	summary of the available groups and categories can be obtained
	with the attributeSummary and filterSummary functions. The
	main use of this is to limit the output of the listAttribute
	and listFilters functions to only selected categories or
	groups. Sequence data can now also be retrieved by the getBM
	function, the getSequence function stays alive as it might be
	easier to use for new biomaRt users.

	Updated getBM to enable retrieval of upstream and downstream
	flanking sequences of a specified length. Removed getOMIM and
	getINTERPRO functions as the same functionality is provided by

	Added column names to output of getSequence. Fixed database
	connection for getSequence when using biomaRt in MySQL mode as
	the host to connect to changed. Fixed requestid for
	identification of biomaRt at the web service.


	Added a basic vignette


	New Package: 

	    This package contains functions for normalizing spotted
	    microarray data, based on a physically motivated
	    calibration model. The model parameters and error
	    distributions are estiamted from external control spikes.

	     Hui Zhao


	Now using lgCMatrix class from Matrix package for the
	representation of the adjacency matrix instead of
	graph-NEL. This should be much more memory and time efficient

	Move nsFilter to genefilter package	

	Better handling for chrom band annotations specified as ranges
	For unexpected range formats, we now try using lcPrefix and
	use that result if there is a non-zero common
	prefix. Otherwise, we fall back to current strategy of
	grabbing just the entire chromosome part.


	Simplification of the Bscore function: remove the step of
	doing a log transformation within 'Bscore' function


	Added 'stackObjects' to generate a stack of
	one-object-per-image images after object detection (many
	people wanted it) and 'tile' to generate a tiled image from a
	stack (e.g. to use in combination with 'stackObjects')


	Added plot parameter to gene.strip

	Added splicing index, gene-exon-probeset reports and enabled
	list output from gene-transcript-exon-probeset translation


	New Package:
		This package implements a broad class of Family Based
		Association Tests for genetics data, with adjustments
		for population admixture using the code from the
		'FBAT' software program (see
		http://www.biostat.harvard.edu/~fbat/fbat.htm). Features
		include: - Uses data from nuclear families, sibships,
		pedigrees, or any combination; provides unbiased tests
		with or without founder genotypes.  - Analyzes
		dichotomous, measured, or time-to-onset traits and
		multiple traits; trait definition can be optimized.  -
		Offers bi-allelic and multi-allelic tests of
		association using standard genetic models (additive,
		dominant, recessive or genotype).  - Offers large
		sample and Monte-Carlo exact tests of the null
		hypothesis: no linkage and no association; offers
		large sample test of H0: no association.  - Estimates
		allele frequencies; checks Mendelian consistency.  -
		Tests multiple markers using haplotypes; estimates
		haplotype frequencies and linkage disequilibrium
		between pairs of markers.  - Offers two multi-marker
		tests for testing multiple markers simultaneously,
		without resolving phase or assuming no recombination.
		- Uses standard pedigree data files; phenotype file is
		optional.  - Offers the Sibs Disequilibrium Test.


		Weiliang Qiu	

	Added checkValidFilenames() to justGCRMA() which ensures that
	'...' picks up celfile names only or passes back a reasonable
	error message
	Changed output of justGCRMA() from an exprSet to an

	Added a 'read.verbose' argument to justGCRMA() to pass to


	New Package:

	    The R Genetics Project is a collaborative effort to
	    develop a complete set of tools for storing, accessing,
	    manipulating, and analyzing genetics data, from small
	    candidate-gene studies consisting of a few genetic markers
	    to large whole-genome studies containing hundreds of
	    thousands of markers.  This package (GeneticsBase)
	    provides a foundation of efficient data structures and
	    easy-to-use manipulation functions.


		Gregory Warnes


	Fix bug in finding the non-null dimnames in graphAM init

	 Bug fix to read.columns, to read SPOT files with a leading
	 column of row numbers. Was failing because the number of
	 headers was less than the number of columns.

	 New tests for topTable() added to limma-Tests.R - bug fix to
	 topTable(). sort="M" and resort.by="M" needed to be updated
	 to sort="logFC" and resort.by="logFC". Also sort="AveExpr"
	 and resort.by="AveExpr" are now allowed.

	Updated addNuId2lumi function to fix a bug when combining
	multiple duplicated probes.

	Make lumiN accept the ExpressionSet inherited objects and data

	Updated lumiN.rsn to allow targetArray to be a vector or
	LumiBatch object


	Deprecated xy2i() and i2xy()


	Added function getChromosomeArm()

	Added intensity.flag for lowess normalisation; added


	Included (1.)  functions for continuous data by Matthias
	Maneck and (2.) new inference methods by Holger
	Froehlich. Almost all functions got changed in the process.

	Started adding help pages


	New Package:
		Parametric Analysis of Gene Set Enrichment

		Karl Dykema


	New Package:

		The package Ringo simplifies the analysis of two-color
		oligonucleotide microarrays from NimbleGen, which for
		example can be used in ChIP-chip projects. The package
		employs functions from various other packages of the
		Bioconductor project and provides additional
		NimbleGen-specific and ChIP-chip-specific
		functionalities. Its mainly covered subjects are data
		read-in, quality control, visualisation and
		identification of genomic regions showing enrichment
		in ChIP-chip. Please take note that Ringo is geared
		towards two-color NimbleGen microarrays. For
		single-channel NimbleGen arrays, we recommend the
		package 'oligo'.


		J. Toedling	


	New Package:

		This package provides mechanisms for automatic
		function prototyping and exposure of R functionality
		in a web services environment.


		Biocore Team


	New, totally revised versions of the EBAM functions. Vignette
	has not been updated yet.


	Interface to logLik now uses default values rather than
	'missing' to decide whether to do normal or profile likelihood
	fixed man page bugs fixed documentation

	Added a method for justvsn for AffyBatch and limma RGLists


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