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Bioconductor Changlog.
Tue, 13 Oct 2009
exonmap
added checking of column names in databases.txt. fixed searches against prediction subset. fixed bug in filtering not working due to column name change in v 50 database.
exonmap
bugfixes to support prediction subset of the database in exon.to.transcript, exon.to.probeset, transcript.to.exon and transcript.to.probeset. Updates to plotting functions - now much faster. Removal of debug option from function parameters.
exonmap
changed post to port in databases.txt column name check
exonmap
fixed bug due to exonmap failing to create db.local directory in exonmap's config directroy (usually .exonmap); changed ordering of parameters in si to better mirror those in 'splicing.index'
exonmap
updated version number
fixed typo in xmapBridge man page that referred to xmapGene
exonmap
Added explicit error message to gene.strip when no exon probesets remain after filtering for multi- and exon-targeting
Added explicit error message to gene.strip when no exon probesets remain after filtering for multi- and exon-targeting
exonmap
made environment checks on package-load less stringent ; now passes R CMD check when package not configured properly. Checks moved to xmapConnect() instead.
exonmap
xmapBridge now checks for species line in config file and warns appropriately if missing
exonmap
changed plot.gene to plotGene; fixed documentation bugs
exonmap
fixed exon.details: bug in warning message when no details found for a given ID
exonmap
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
Put package version numbers in standard x.y.z format.
exonmap
Significant overhaul. Gor rid of platform specifics in path names. Refactored code. Unified function call parameters. Made output from related functions more consistent. Changed the way databases are specified. Improved speed of filtering functions. Updated vignettes.
exonmap
fixed client flag must be integer bug with recent versions of RMySQL
exonmap
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
exonmap
fixed warnings if xmapConnect() called twice in a row.
exonmap
allowing for more consistent num_probes column names in database
handling database queries with NULL as the database id
exonmap
Updated eSet object and bumped version number.
exonmap
made sure port number is passed to MySQL as an integer
exonmap
Changed biocViews entry of Statistics to Bioinformatics.
exonmap
Fixed the code/documentation mismatch in probeset.stats.Rd:
in the usage and argument sectiosn, change probeset.stats(probeset) to
probeset.stats(v) to match the name of the argument described in the
code (probeset.stas <- function(v){...}.
Bumped the version to 2.3.2.
exonmap
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
bumped version number
exonmap
Improved handling of NULL/empty lists as parameter to search/filtering functions. Compatibility changes for next release of X:Map. Bug fix to support database change during session.
exonmap
Replace support for soon to be defunct class exprSet with ExpressionSet.
exonmap
Fixed malformed depends field: change RMySQL (>=0.6-0) to RMySQL (>=
0.6-0)
exonmap
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
exonmap
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
exonmap
change in column name in v50 was breaking gene.to.exon.probeset. Fixed.