CHANGES IN VERSION 3.7.1 ------------------------ USER VISIBLE CHANGES o Added a population of scores with 2-decimal places of precision. See methods 'populations()' and 'defaultPopulation()'. o Added metadata on tag and group annotations for automatic manipulation of the scores. See methods 'gscoresTag()' and 'gscoresGroup()'. o Added metadata on the total number of sites with scores. See method 'nsites()'. CHANGES IN VERSION 3.6.0 ------------------------ USER VISIBLE CHANGES o Added citation metadata available through the GScores object and the 'citation()' method. CHANGES IN VERSION 3.5.0 ------------------------ USER VISIBLE CHANGES o The class definition and methods that support access to this annotation package have been moved from the VariantFiltering package to the GenomicScores package. o Missing phastCons scores were coded as 0 in versions <= 3.4 and now are coded as NAs. CHANGES IN VERSION 3.2.0 ------------------------ USER VISIBLE CHANGES o An update in the in the VariantFiltering package scores() function enables a 10-fold faster retrieval of mean phastCons scores over genomic intervals. CHANGES IN VERSION 3.1.0 ------------------------ USER VISIBLE CHANGES o Updated phastCons scores to the UCSC available data on March 2015 o Individual files storing phastCons scores per chromosome within the 'extdata' directory of the package are now stored and loaded using the saveRDS() and readRDS() functions instead of classical save() and load(). Corresponding filenames have now an '.rds' extension and the chromosome name is written now at the end of the filename, right before '.rds'. CHANGES IN VERSION 3.0.0 ------------------------ USER VISIBLE CHANGES o Updated phastCons scores to the UCSC available data on October 2014 o Instead loading in main memory the set of phastCons scores for the entire human genome, they are now stored separetely by chromosome and they are loaded and cached into main memory as different chromosomes get accessed to reduce the memory footprint at package loading time. Caching may be disabled, and thus memory footprint minimized, setting a new argument 'caching=FALSE' in the 'scores()' function, at the cost of slowing down multiple calls to the 'scores()' function. CHANGES IN VERSION 0.99.1 ------------------------- USER VISIBLE CHANGES o Submission of the first version to the Bioconductor project. (start date: 15 April, 2014)