[Bioc-devel] NEWS April 2007

[James MacDonald]

	April 2007

ACME

	Fixed chi-square calculation a bit to be actual counts in the
	cells rather than the counts of the marginals in a couple of
	cells.

	Fixed bug in write.sgr when colnames were not defined on vals


affy

	Added 'cdf' argument to xy2indices() and indices2xy() so those
	without an AffyBatch can still map things. The cdf argument in
	this case is simply the name of the requisite cdf package.

	
affycoretools

	Bugfix to vennSelect() when the number of probesets == 1


affyio

	Fixed issue with non-square cel file parsing using binary (xda)
	format cel files.  The Affymetrix documentation is
	inconsistent with the reality (rows, cols swapped).


annaffy
	
	Fixed GO links


AnnBuilder

	Updated AnnBuilder to accommodate the changes to KEGG website.

	Added support for Bos taurus and fixed parsing routine for
	GENENAME

annotate

	Fixed GO helper functions to deal with missing NA entries.

	Use sample.ExpressionSet data for Pretty Output vignette

AnnotationDbi

	Changes to demo vignette to compare env and SQLite based
	annotation packages

	Add a revmap method for environment objects This allows revmap
	to be used on environment-based ann pkgs

	Added man pages for 'db_conn' and 'db_file' to HGU95AV2DB
	template

beadarray

	Changed readBeadSummaryData to read BeadStudio V2 output

	CreateBeadSummaryData now assigns array names to the columns
	of the intensity data - 'pData' and 'phenoData' now defined
	for BeadLevelList - added 'targets' argument to qcPlots and
	updated man page

bgx

	New Package:
	    Bayesian integrated analysis of Affymetrix GeneChips

	Maintainer:
	     Ernest Turro


Biobase

	listLen now returns an integer vector (rather than numeric)
	and I also tried to better the documentation

	Further refinement of listLen In package code, INTEGER() is a
	function, so it is better to call it only once. Also improved
	the error message to give more information and added some
	detail to the man page.

	Add ScalarCharacter class This is a utility class that can be
	used to ease validation burden when writing classes that
	require a string slot.

	Add assayDataElement<- function

	Add readExpressionSet, deprecate read.exprSet, read.phenoData

	Changed welcome message

biocGraph

	New Package:
	    This package provides examples and code that make use of
	    the different graph related packages produced by
	    Bioconductor.

	 Maintainer:
	    Li Long

biomaRt

	Fixed listAttributes function

	Removed array argument from getGene, getFeature and getGO as
	affymetrix arrays can now be specified using the type argument
	of these functions. Removed to.array and from.array arguments
	from getHomolog function as the affy arrays can be specified
	using the from.type and to.type arguments. To extend the
	possible types of identifiers that can be used for the
	getGene, getGO,etc functions, the value for the type argument
	has to be a filter given by the listFilters function.

	Updating handling of BooleanFilters. Whenever the user now
	uses a boolean filter a value of 1 or 0 will have to be
	specified to indicate true or false. To see if a filter is
	boolean the user can run listFilters with the showType
	argument = TRUE.

	Slimmed the listDatasets function, and it now returns a
	dataframe with character columns rather than factors

	Added specification of the web server port. Two new BioMarts
	don't use the default port 80 and were not accessible before
	this fix.

	Rewrote XML parsers to make code cleaner. Added detection of
	filter options. Some filters have a predetermed set of values
	and now these can be shown using the filterOptions
	function. Added the function filterType so users can determine
	the type of a filter (is important to know which filters are
	booleans). Updated vignette with the two new functions.

Biostrings

	Replaced slots "start" (integer), "end" (integer) and "desc"
	(character) by single slot "views" (data frame with cols
	"start", "end" and "desc") in "BStringViews" class definition
	 
	 Added the matchProbePair() function

	 Made matchProbePair() a new generic instead of a
	 function. Default for 'baseOnly' arg in alphabetFrequency()
	 is now FALSE instead of TRUE. Deprecated as.complex() in
	 favor of toComplex()

BufferedMatrix

	Changed median.polish.summarize.BufferedMatrix to
	median.polish.summarize

Category

	Expose makeChrBandGraph. This patch also fixes the root node
	so that it does not contain all annotations.

	Add chrBandInciMat and makeChrBandInciMat functions

	Add geneIdsByCategory and doc

	Move sigCategories to Category and make it a generic

	Fix bug in hyperGTest for ChrMapHyperGParams objects R's
	intersect(x, y) function returns a vector with mode matching y
	if x and y have different modes. The bug was the result of
	assuming that standard coerce rules apply. They don't in this
	case as is documented in the intersect man page.

cellHTS
	
	Fixed a bug in the read function (that didn't seem to have an
	effect in previous R versions), and made the verbose output a
	bit prettier

copa

	Small change in copaPerm() that speeds the operation by about
	a gazillion-fold. Thanks to Laurent Gaultier for pointing this
	out.

CORREP

	New Package:
	    Multivariate correlation estimation and statistical
	    inference. See package vignette.

	Maintainer:
	    Dongxiao Zhu


DNAcopy

	Added code to not split if maximal statistic is small (<= 0.1)
	and split if it is large (>= 7) without computing the
	p-values.

	Added warning that windowing code wil be deprecated in version
	1.11

flowCore

	Updated Subset for new multiple filter options. Also fixed
	filterSummary

	Big changes to HowTo vignette. * Minor changes to coercion and
	read.flowSet to address Errol's troubles. * Removed as()<-. I
	guess Seth will be happy. * Minor documentation changes * A
	couple of small bugs with split * A $ accessor for flowSets

GEOquery

	 Updated GDS2eSet to return an object of class ExpressionSet
	 instead of the old exprSet

	 
GOstats
	
	Fixup and document termGraph, inducedTermGraph, and
	plotGOTermGraph

	Fixed up the compGdist function a bit

	Modification to probeSetSummary() to allow end users the
	option of passing a vector of probeset IDs so the output of
	this function actually counts _all_ probesets that contributed
	to a significant GO term.

graph

	Fix subGraph attribute handling for graphNEL This needs to be
	generalized for all subGraph methods. This patch adds proper
	handling of node and edge attributes for the subGraph
	operation.  Before, we copied all attributes and now we only
	copy over the appropriate subset.

	Fix documentation of graphNEL class

	addEdge for graphNEL warns if edge already exists Note that
	for graphAM, this is an error. We warn when replacing an
	already existing edge using addEdge because in the past some
	users used graphNEL for representing non-simple graphs with
	multi-edges. Since this is no longer supported, a warning
	message is helpful.

limma

	limma 2.9.17 - bug fix to read.maimages() for
	source="arrayvision". Now reads arrayvision files again for
	the first time since version 2.3.1.

makecdfenv

	Modified make.cdf.packages() to create an additional
	environment with the usual package name appended with 'dim'
	(e.g., hgu95av2dim) that contains the chip dimensions. This is
	intended to be used by indices2xy() and xy2indices() in the
	affy package as a replacement for the deprecated xy2i() and
	i2xy() functions.

Mfuzz

	Bug in mfuzz.plot2 fixed

pcaMethods
	
	Added a svd method that is robust to outliers. Also a pca
	method based on this robust svd.

	Added vingette discussing handling of data with outliers

	nipals(center=T) was also accidentially sclaing the data, as
	we used scale(data, center=T).  This has been fixed.
	
	svnImpute returned too many scores/loadings, this was
	fixed. And now we also assign correct row/column names to
	scores/loading matrices

prada

	Fixed bug in drawGate when adding additional regions

puma

	New Package:
	    Most analyses of Affymetrix GeneChip data are based on
	    point estimates of expression levels and ignore the
	    uncertainty of such estimates. By propagating uncertainty
	    to downstream analyses we can improve results from
	    microarray analyses. For the first time, the puma package
	    makes a suite of uncertainty propagation methods available
	    to a general audience. puma also offers improvements in
	    terms of scope and speed of execution over previously
	    available uncertainty propagation methods. Included are
	    summarisation, differential expression detection,
	    clustering and PCA methods, together with useful plotting
	    and data manipulation functions.

	 Maintainer:
	     Richard Pearson

reb

	Added movt() - a moving t-test method for reb()

Rgraphviz

	deprecate imageMap

	rename LLagopen to agopenSimple

RWebServices

	Provide more informative error messages when Java -> R data
	tests go wrong

	Add indexNA in RComplex and RNumeric, and modify convert
	functions correspondingly. We tried to use NaN to represent
	both NaN and NA for R complex and R numberic vectors in
	Java. Now we seperate those two concepts. * change the java
	class name that represents all functions in a package from
	<package>.java to <package>Function.java

siggenes

	EBAM updated, added new vignette

	Posterior probabilities are truncated at zero

tilingArray
	
	Updated function segChrom and segmentation vignette

	
xcms

	Modified findPeaks method: - Moved column "i" (peak number
	within combined EIC) to the second-to-last column - Added
	column "sn" with signal to noise ratio xcmsSets now include
	"i" and "sn" columns in the peaks matrix

	Added : - rawEIC method - findMZBoxes method -
	findPeaks.centWave method Modified findPeaks() method to
	support different findPeaks.* algorithms

	Added some lines concerning findPeaks.centWave to the
	vignette, changed output of centWave to matrix instead of
	data.frame

	Removed formerly deprecated function clustunique() Changed
	xcmsEIC plotting function from an S4 to an S3 method Removed
	all instances of isGeneric()

	



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