************************************************** * * * 1.6.x SERIES NEWS * * * ************************************************** OrganismDbi VERSION 1.6.x NEW FEATURES o genes method now works on these objects BUG FIXES o safer argument handling for 'by' arguments on accessors that use it. ************************************************** * * * 1.4.x SERIES NEWS * * * ************************************************** OrganismDbi VERSION 1.4.x NEW FEATURES o keys method now has new arguments to allow for more sophisticated filtering. BUG FIXES o cols arguments and methods will now be columns arguments and methods o stricter argument checking for select and friends ************************************************** * * * 1.2.x SERIES NEWS * * * ************************************************** OrganismDbi VERSION 1.2.x NEW FEATURES o There are now range based accessors (transcripts, exons, cds) that can be used to get data out of OrganismDb objects. o There are now list oriented range based accesors (transcriptsBy, exonsBy, cdsBy) that can be used to get data out of OrganismDb objects o All these new ranged based operations allow users to extract additional metadata via mcols slot in the resulting object. The extra data is specified via the columns argument to these methods. SIGNIFICANT USER-VISIBLE CHANGES o New range based accessors allow you to get data back organized by range. Please see associated manual pages and vignette for more details. BUG FIXES o Show method for these objects is improved. o Documentation, tests and vignette updates for new methods. ************************************************** * * * 1.0.0 SERIES NEWS * * * ************************************************** OrganismDbi VERSION 1.0.0 PKG FEATURES o OrganismDbi is for the creation and support of a new class of super-annotation packages o 'Stock' OrganismDbi packages are available for human mouse and rat with the 2.11 release of Bioconductor. o OrganismDbi has functionality for generating these packages. o OrganismDbi has methods that allow these packages to function. o OrganismDbi works by combining resources from Annotation packages that implement the four methods needed for a "select" style interface. The essense of this is detailed in the AnnotationDbi package, along with base classes etc.