- Version 1.5.5: Added weighted option to compute distances between objects when replicates are available ### Package suffered major revisions since version 1.3 ### Major changes from Version 1.3, mainly affecting the clusGPS function - Removed existing distance transformation before clustering if no clustering object was provided - Changes in the behaviour of clusGPS function, it can only be used with an external precomputed clustering object now - Added preMerging to clusGPS step to ensure a minimum epigenetic cluster size - Added function mergeClusters to perform unsupervised cluster merging based on spatial overlap and changepoint detection - Posterior probabilities of clusters are now adjusted on the fly (much faster) - Posterior probabilities are now weighted according to the size of each cluster - New function to profile epigenetic clusters - Moved grid density calculation out of clusGPS function - Updated plot method for clusGPS objects Other changes from Version 1.3 - Added function to export chroGPS maps to Cytoscape - Added dynamic vignette with code for replicating toy analysis - Added accessor functions for S4 classes - Added stress measure for goodnes-of-fit of MDS objects - Fixed bugs in R-Square calculation of some distance metrics - Changed the available data object and object names - Introduced mahalanobis distance in distGPS - Updated examples and documentation - Fixed bug in boostMDS, not properly using random seed in all cases Major changes in Version 1.20 - Replaced GRanges/GRangesList class with GRanges/GRangesList