CHANGES IN VERSION 1.18.0 ----------------------- NEW FEATURES o Expanded toGRanges support. It is now possible to transform coverage objects (i.e. toGRanges(coverage(A))) into GRanges. It also supports ".assoc" files produced by PLINK. o overlapPermTest now supports multiple region sets in B and will perform a multi- permutation test against each one much faster than testing them independently. BUG FIXES o Multiple bug fixes CHANGES IN VERSION 1.13.2 ----------------------- BUG FIXES o createRandomRegions ignored the non.overlapping argument. It does work now. CHANGES IN VERSION 1.13.1 ----------------------- NEW FEATURES o Revamped toGRanges now accepts genome region descriptions as used by UCSC and IGV ("chr9:23000-25000"). It also may take a genome parameter and set the genome information of the GRanges accordingly. CHANGES IN VERSION 1.9.2 ----------------------- NEW FEATURES o Simplified the interface of toGRanges for simpler use when manually creating GRanges. Now toGRanges("chr1", 10, 20) is valid. BUG FIXES o Multiple minor bug fixes CHANGES IN VERSION 1.1.8 ----------------------- NEW FEATURES o Added new functionality to permTest to use multiple evaluation functions with a single randomization procedure. This gives a significant speedup when comparing a single region set with multiple other features o Created a new function createFunctionsList() that given a function and a list of values, creates a list of curried functions (e.g with one parameter preassigned to each of the given values) PERFORMANCE IMPROVEMENTS o Complete rewrite of randomizeRegions() resulting in a 10 to 100 fold speedup BUG FIXES o Multiple minor bug fixes