Changes in version 1.2.4 (2015-01-21) ------------------------------------- OTHER o update package maintainer Changes in version 1.2.3 (2015-01-20) ------------------------------------- BUG FIXES o createBins() now also works for species not supported by GenomeInfoDb (such as Canis lupus familiaris) Changes in version 1.2.2 (2014-12-23) ------------------------------------- IMPROVEMENTS o applyFilters() now ignores the residual filter for chromosomes for which it does not exist (instead of always filtering out the entire chromosome) Changes in version 1.2.1 (2014-11-01) ------------------------------------- IMPROVEMENTS o add an asterisk in the noise measure to clarify it's not a regular standard deviation or variance, but first scaled with the mean (so that the mean is 1.0 and the relationship holds between variance and 1/N, where N is the average number of reads per bins) o clarify the use of log2/sqrt transformation in segmentBins() Changes in version 1.2.0 (2014-10-14) ------------------------------------- RELEASE o Bioconductor 3.0 IMPROVEMENTS o segmentBins() supports another transformation option besides log2: sqrt(x + 3/8), which stabilizes the variance o plot() can skip plotting of segments and calls by specifying doSegments=FALSE and doCalls=FALSE o exportBins() also supports BED files BUG FIXES o exportBins() saves base pair positions in fixed notation instead of scientific Changes in version 1.0.5 (2014-06-13) ------------------------------------- BUG FIXES o fix a bug caused by package matrixStats changing madDiff() from an S4 to an S3 method in version 0.9.4, released on 2014-05-23 Changes in version 1.0.4 (2014-05-23) ------------------------------------- BUG FIXES o getBinAnnotations() fixed after being broken by a change in Bitbucket Changes in version 1.0.3 (2014-05-23) ------------------------------------- IMPROVEMENTS o added exportBins() for exporting to a file o switch graphics in the vignette to PNG Changes in version 1.0.2 (2014-05-15) ------------------------------------- IMPROVEMENTS o plot() honors user-specified values for xlab and xaxt o plot() allows omission of labels for the standard deviation and the number of data points o improve diagnostic messages Changes in version 1.0.1 (2014-04-17) ------------------------------------- BUG FIXES o smoothOutlierBins() correctly ignores bins filtered out Changes in version 1.0.0 (2014-04-14) ------------------------------------- RELEASE o initial release as part of Bioconductor 2.14