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Bioconductor Changlog.
Wed, 24 Jun 2009
GSEABase
Update imports
toBroadSet now works with current XML
GSEABase
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
GSEABase
Changed biocViews entry of Statistics to Bioinformatics.
GSEABase
belated update to NEWS
GSEABase
update getBroadSet with examples for retrieving from msigdb.xml or c*.gmt
GSEABase
correct man page mis-identifier assignment (thanks Vince)
GSEABase
GeneSetCollection,ExpressionSet,(Pfam|Prosite|Chrloc)Collection-method
- correct dispath
update valid evidenceCodes
GSEABase
minor documentation type -- should be getGmt
GSEABase
minor documentation type -- should be getGmt
GSEABase
Correct manual page markup
GSEABase
Add small GeneSetCollection construction example from KEGG ids
GSEABase
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
GSEABase
Add ENSEMBLIdentifier
GSEABase
Add missing method documentation
GSEABase
Version bump for new generics
GSEABase
Explicitely defining generics for 'geneIds', 'geneIds<-' and 'ontology' now and exporting them in the namespace. The definition of 'geneIds' has been extended by '...'
GSEABase
toGmt, getGmt write to and read from GMT gene set file formats
GSEABase
Depends; graph rather than Imports; importFrom(graph, union)
- further check-in revising unit test code
Depends; graph rather than Imports; importFrom(graph, union)
- Depends since OBO's can be coerced to graphNEL objects
- reuse union generic because this seems to be necessary for R CMD
check, https://stat.ethz.ch/pipermail/r-devel/2008-June/049933.html
GSEABase
parse new broad xml
GSEABase
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
GSEABase
Update unit tests to match new annotation packages
- future goal: make unit tests more independent of specific maps
GSEABase
API and other changes necessary to pass R CMD check without error
- GeneSet construction from GOCollection requires a geneIdType arugment
- GOCollection provided with optional arugment err=FALSE controlling
consequences of missing identifiers
GSEABase
updateObject for outdated serialized instances
- 'annotation' generates an error advising that updateObject needs to
be called
- updateObject,GeneSetCollection calls updateObject on all objects,
then re-initializes the GeneSetCollection
mapIdentifiers,GeneColorSet,*-methods exception test and tidy
- new unit test
- revised error message on failure
- tidy of mapIdentifiers man page
GSEABase
mapIdentifiers,GeneColorSet,*-methods exception test and tidy
- new unit test
- revised error message on failure
- tidy of mapIdentifiers man page
implement mapIdentifiers,GeneColorSet,*-methods
- account for many-to-1, 1-to-0, 1-to-many mappings with gene- and
phenotype colors
Correctly check for existence of generics before creating getter and
setter methods
- 'Getters' and 'setters' were creating a generic because none existed
in the package namespace, but should have been checking on the
package search path (no 'where' argument in 'isGeneric').
GSEABase
Significant changes to GeneIdentifierType and GOCollection
- (optional) 'annotation' slot added to all GeneIdentifierType
classes.
- mapIdentifiers now more flexible -- trying to map between any two
types within an annotation package
- ontology added to GOCollection
- No depdendcy on GO package for vignette, just GO.db
GSEABase
Significant changes to GeneIdentifierType and GOCollection
- (optional) 'annotation' slot added to all GeneIdentifierType
classes.
- mapIdentifiers now more flexible -- trying to map between any two
types within an annotation package
- ontology added to GOCollection
- No depdendcy on GO package for vignette, just GO.db
GSEABase
export annotation<-
GSEABase
Add mapIdentifers,GeneIdentifierType,AnnDbBimap-method to allow
user-supplied AnnDbBimaps
Depend but don't Import AnnotationDbi, Biobase; not sure whether
AnnotationDbi should be Import instead of Depend
GSEABase
Added mapIdentifers,AnnotationIdentifier,AnnotationIdentifer-method as null map
GSEABase
Add MapCollection documentation alias
Export MapCollection class
GSEABase
Further rely on getAnnMap and automatic annotation package selection;
Minor documentation tidy
GSEABase
Further rely on getAnnMap and automatic annotation package selection;
Minor documentation tidy
Add 'NEWS' file
Supply missing documentation for Logic methods
GSEABase
Updating the license reference to reflect R standards.
GSEABase
* Remove 'names' attribute from lists used to construct gene sets
This is important with sapply(gsc[2], ...) for instance, where the
names attribute is (a) subsetted incorrectly and (b) used by sapply,
GSEABase
Add ComputedCollection class, and use for result of logic operations
- CollectionType Logic CollectionType --> CollectionType when identical
- all others, including identical CollectionIdType, lead to ComputedCollection
GSEABase
GeneSetCollection constructors from character vector of gene ids
- GeneSetCollection,character,AnnotationIdentifier,CollectionType-method
- GeneSetCollection,character,AnnotationIdentifier,CollectionIdType-method
- use getAnnMap with GeneSetCollection, rather than .getAnnMap
- documentation tidy