Version 1.1.5
- Added missing documentation
Version 1.1.4
- Fixed bug in cmds for method with empty chromosomes
Version 1.1.3
- Fixed bug in alignPeaks (no longer directly accessing matchMatrix slot of RangesMatchingList object)
- Added plotMeanCoverage
- Fixed bug in gini for method with no chromosome lengths
Version 1.1.2
- Add methods for objects of class GRanges and GRangesList.
- Add set.seed to vignette.
- Use pvec instead of mclapply in tabDuplReads and filterDuplReads.
- Correct rpkm form enrichedRegions and remove it from enrichedPeaks
- Fixed giniCoverage for ranges with low numbers of reads
Version 1.1.1
- Adjusted parallel computing in enrichedPeaks so that it no longer spans an uncontrolled number of child processes when mc.cores>1
- Added arguments "labels" and "cex.text" to the plot method for cmdsFit objects.
- Added monotonicity contraint to filterDuplReads and fdrEnrichedCounts to ensure that the estimated FDR decreases with the number of repeats
- Fixed overflow problem in enrichedChrRegions which occurred for long genomes (e.g. human)
- Adjusted behavior of stdPeakLocation so that it is consistent with PeakLocation
- Fixed bug in RPKM calculation by enrichedRegions
- Added option to compute Spearman correlations in cmds
- Fixed bug in enrichedChrRegions line 54
