*****版本1.99.1 - 2013年1月23日·更新后用于Bioconductor 3.1 *****版本1.7.2 - 2013年1月23日。filterFFT-methods.R改变。现在区域过滤在迭代循环中执行，而不是通过递归调用。这极大地提高了未分割的长区域的内存使用。*****版本1.5.0 - 2012年10月1日。从多核更改为并行包*****版本1.2.2 - 2012年3月23日。'mergeCalls'现在使用参数'min.overlap'而不是'dyad。dist'，因为它与来自伊朗的计数重叠电话一致。'peakDetection'崩溃时，没有值低于阈值*****版本1.2.1 - 2012年3月1日。修正了'mergeCalls'函数的内存使用和速度。 Added scale factor and other parameters to 'coverage.rpm' ***** version 1.2.0 - 15 November 2011 + Added 'mergeCalls': automatic merging of close nucleosome calls . Individual height and width score are returned in peakScoring, additionally to the mixed score . PlotPeaks has now support for fuzzy nucleosomes and decomposite score . Fixed malfunction of processReads in single-ended reads when using trim==fragmentLen ***** version 0.99.7 - 27 October 2011 (v.1.0RC2 for BioC 2.9) . Improved performance (CPU and memory need) of fragmentLenDetect for large (human-ENCODE) datasets. ***** version 0.99.6 - 24 October 2011 (v.1.0RC for BioC 2.9) . Changed the score system in peakScoring for ranged data. Now different weigths for width and height score can be specified and the weighted sum of the scores is returned, instead the direct product of them. ***** version 0.99.5 - 13 October 2011 . Bug fix in the fragmentLenDetect which was returning wrong values, processReads could also be affected by this bug + processReads: Added custom parameters pass for fragmentLenDetect if fragmentLen=NULL + fragmentLenDetect: Added parameter as.shift to allow shift value return instead of the fragment length (the one by default) ***** version 0.99.4 - 01 August 2011 + "threshold" in peak calling now can be set using percentage or a direct coverage value . export.wig now only uses maximum 4 decimals to avoid creating big size wig files . bugfixes in export.wig and export.bed . increased default threshold for pcKeepCompDetect (old value was too restrictive) ***** version 0.99.3 - 19 July 2011 . bug fixes ***** version 0.99.2 - 17 July 2011 + First version available in Bioconductor + CITATION file added . filterFFT now returns a NA or 0 value in the same regions as the input has it . pcKeepCompDetect now returns a value in the range pc.min:pc.max ***** version 0.99.1 - 11 July 2011 + Added pcKeepCompDetect (automatic calculation of fitted component selection for filterFFT) + Added controlCorrection (correction of coverage profiles to avoid methodology biases) . Correction of "multicore" library detection . Correction of a bug in the filterFFT in joining large sequences . filterFFT now takes as default pcKeepComp="auto" . pcKeepCompDetect and controlCorrection added to vignette ***** version 0.99.0 - 28 june 2011 . Minor changes to satisfy Bioconductor requirements ***** version 0.2.1 - 27 april 2011 + Added example code to all functions . Fixes in export.wig function ***** version 0.2.0 - 18 april 2011 + Added fragmentLenDetect (automatic calculation of sequenced fragments for single ended data) + Added syntheticNucMap (generation of random coverage maps) . Minor corrections in other functions **** version 0.1.3 - 02 february 2011 + First public version