[Bioc-devel] NEWS March 2007
James MacDonald
jmacdon at med.umich.edu
Wed Apr 4 16:55:15 CEST 2007
March 2007
ACME
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.
Maintainer:
Sean Davis
affxparser
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
names.
affy
updateObject() now removes empty or inconsistent se.exprs from
AffyBatch objects
Return new('matrix') rather than NULL if se.exprs undefined
AnnBuilder
Updated GO url, fixed bug in getGOUrl()
annotate
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
AnnotationDbi
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()
beadarray
Bugfix to qcBeadLevel() and new arg experimentName for HTML
report heading
biomaRt
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
getBM
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.
BufferedMatrix
Added a basic vignette
CALIB
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.
Maintainer:
Hui Zhao
Category
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.
cellHTS
Simplification of the Bscore function: remove the step of
doing a log transformation within 'Bscore' function
EBImage
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')
exonmap
Added plot parameter to gene.strip
Added splicing index, gene-exon-probeset reports and enabled
list output from gene-transcript-exon-probeset translation
functions
fbat
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.
Maintainer:
Weiliang Qiu
gcrma
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
ExpressionSet
Added a 'read.verbose' argument to justGCRMA() to pass to
read.probematrix()
GeneticsBase
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.
Maintainer:
Gregory Warnes
graph
Fix bug in finding the non-null dimnames in graphAM init
limma
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.
lumi
Updated addNuId2lumi function to fix a bug when combining
multiple duplicated probes.
Make lumiN accept the ExpressionSet inherited objects and data
matrix
Updated lumiN.rsn to allow targetArray to be a vector or
LumiBatch object
makecdfenv
Deprecated xy2i() and i2xy()
MANOR
Added function getChromosomeArm()
Added intensity.flag for lowess normalisation; added
pct.spot.before.qscore()
nem
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.
oligo
Started adding help pages
PGSEA
New Package:
Parametric Analysis of Gene Set Enrichment
Maintainer:
Karl Dykema
Ringo
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'.
Maintainer:
J. Toedling
RWebServices
New Package:
This package provides mechanisms for automatic
function prototyping and exposure of R functionality
in a web services environment.
Maintainer:
Biocore Team
siggenes
New, totally revised versions of the EBAM functions. Vignette
has not been updated yet.
vsn
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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