NEWS

---

biomvRCNS 1.3.3

NEW FEATURES

• updates in package vignette

BUG FIXES

• remove limitation of maximum typecode in the plot, now using rainbow()

biomvRCNS 1.3.2

BUG FIXES

• fix the returned posterior p

biomvRCNS 1.1.9

BUG FIXES

• NA bug when model fails
• using the length of the segment if shorter than maxk

biomvRCNS 1.1.8

NEW FEATURES

• add error catching in biomvRhsmm
• updates in package vignette

BUG FIXES

• fine tuning of memory usage for large count data structure
• minor bug fixes

biomvRCNS 1.1.7

NEW FEATURES

• add support of Rle like sparse data in mcols of large count data structure.
• add mclapply for parallel processing of different seqnames in biomvRhsmm

biomvRCNS 1.1.6

BUG FIXES

• fix nbinom emis estimateSegCommonDisp -> nbinomCLLDD

biomvRCNS 1.1.5

NEW FEATURES

• update biomvRGviz to have trackList returned when tofile=FALSE

BUG FIXES

• typo fix in function argument

biomvRCNS 1.1.4

NEW FEATURES

• update biomvRGviz to plot multiple samples in one, and more param
• plot method now defaults to multiple samples in one, sampleInOne=T

BUG FIXES

• fix states rank when prior.m=cluster

biomvRCNS 1.1.3

NEW FEATURES

• the x slot in the returning object for biomvRhsmm now also contains the probability of associated state for each position
• the param slot in the returning object for biomvRhsmm now also contains the updated emission and sojourn parameters for each seqname and sample column

biomvRCNS 1.1.2

NEW FEATURES

• add a new clustering method for emission prior estimation
• add a new example section of DMR detection in the vignette

BUG FIXES

• switch off several data checking warnings, use normal cat() instead

biomvRCNS 1.1.1

NEW FEATURES

• add support of direct input of sojourn parameters as named list.

BUG FIXES

• suppress warnings generated when appending GRanges object for the output

biomvRCNS 0.99.3

NEW FEATURES

• add mvt and t to the emis.type and tmvtFit function

BUG FIXES

• fix shift index (-1) in pois and nbinom fitting

biomvRCNS 0.99.2

NEW FEATURES

• add log-Vertibi in c
• add normalizing factor for estimation of emis$p and soj$d
• add avgFunc to be used in average calculation, median and mean with trim, default to median

BUG FIXES

• fix shift index (-1) in pois and nbinom fitting

biomvRCNS 0.99.1

NEW FEATURES

• in Bioc-devel