CHANGES IN VERSION 1.3.3 ------------------------- NEW FEATURES o updates in package vignette BUG FIXES o remove limitation of maximum typecode in the plot, now using rainbow() CHANGES IN VERSION 1.3.2 ------------------------- BUG FIXES o fix the returned posterior p CHANGES IN VERSION 1.1.9 ------------------------- BUG FIXES o NA bug when model fails o using the length of the segment if shorter than maxk CHANGES IN VERSION 1.1.8 ------------------------- NEW FEATURES o add error catching in biomvRhsmm o updates in package vignette BUG FIXES o fine tuning of memory usage for large count data structure o minor bug fixes CHANGES IN VERSION 1.1.7 ------------------------- NEW FEATURES o add support of Rle like sparse data in mcols of large count data structure. o add mclapply for parallel processing of different seqnames in biomvRhsmm CHANGES IN VERSION 1.1.6 ------------------------- BUG FIXES o fix nbinom emis estimateSegCommonDisp -> nbinomCLLDD CHANGES IN VERSION 1.1.5 ------------------------- NEW FEATURES o update biomvRGviz to have trackList returned when tofile=FALSE BUG FIXES o typo fix in function argument CHANGES IN VERSION 1.1.4 ------------------------- NEW FEATURES o update biomvRGviz to plot multiple samples in one, and more param o plot method now defaults to multiple samples in one, sampleInOne=T BUG FIXES o fix states rank when prior.m=cluster CHANGES IN VERSION 1.1.3 ------------------------- NEW FEATURES o the x slot in the returning object for biomvRhsmm now also contains the probability of associated state for each position o the param slot in the returning object for biomvRhsmm now also contains the updated emission and sojourn parameters for each seqname and sample column CHANGES IN VERSION 1.1.2 ------------------------- NEW FEATURES o add a new clustering method for emission prior estimation o add a new example section of DMR detection in the vignette BUG FIXES o switch off several data checking warnings, use normal cat() instead CHANGES IN VERSION 1.1.1 ------------------------- NEW FEATURES o add support of direct input of sojourn parameters as named list. BUG FIXES o suppress warnings generated when appending GRanges object for the output CHANGES IN VERSION 0.99.3 ------------------------- NEW FEATURES o add mvt and t to the emis.type and tmvtFit function BUG FIXES o fix shift index (-1) in pois and nbinom fitting CHANGES IN VERSION 0.99.2 ------------------------- NEW FEATURES o add log-Vertibi in c o add normalizing factor for estimation of emis$p and soj$d o add avgFunc to be used in average calculation, median and mean with trim, default to median BUG FIXES o fix shift index (-1) in pois and nbinom fitting CHANGES IN VERSION 0.99.1 ------------------------- NEW FEATURES o in Bioc-devel