Changes in version 1.12.0
-------------------------
RELEASE
o Bioconductor 3.5
IMPROVEMENTS
o VCF and SEG file export have been implemented to allow use of
downstream analysis tools such as Cartegenia (NGS) Bench.
o binReadCounts() now supports parallel computing
o calculateBlackListByRegions() has been implemented for convient
bin overlap calculation of any set of regions.
Changes in version 1.10.0
-------------------------
RELEASE
o Bioconductor 3.4
Changes in version 1.8.0 (2016-05-04)
-------------------------------------
RELEASE
o Bioconductor 3.3
IMPROVEMENTS
o estimateCorrection(), segmentBins(), createBins(), and
calculateBlacklist() now support parallel computing
(see vignette for more details)
o callBins() can now also use cutoffs instead of CGHcall
o binReadCounts() now contains parameter pairedEnds to specify when using
paired-end data, so that expected variance can be calculated correctly
o segmentBins() now allows seeds for random number generation to be
specified for reproducibility
o binReadCounts() supports chunked processing of bam files
o estimateCorrection() now also allows correcting for only GC content or
mappability
BUG FIXES
o applyFilters() and highlightFilters() now work properly when using a
numerical value for parameter residual
o highlightFilters() no longer highlights entire chromosomes for which
the residual filter is missing altogether, which matches the behavior of
applyFilters()
o getBinAnnotations() now allows custom bin annotations to be loaded via
the path parameter even when an annotation package has been installed
o phenodata files with a single variable are now handled correctly
o calculateMappability() now retains correct chromosome order even when
bigWigAverageOverBed reorders them
o calculateBlacklist() now correctly handles non-integer chromosome names
Changes in version 1.6.0 (2015-10-14)
-------------------------------------
RELEASE
o Bioconductor 3.2
IMPROVEMENTS
o chromosomes() no longer tries to return chromosome names as an integer
vector, but returns a character vector instead
BUG FIXES
o plot() and calculateMappability() now work also for other chromosome
names besides numbers and "X", "Y", and "MT"
Changes in version 1.4.2 (2015-08-20)
-------------------------------------
BUG FIXES
o createBins() now properly selects chromosomes when ignoring
mitochondrial DNA. Please note that the mitochondrial DNA is only
ignored when it is called either "chrMT", "chrM", "MT", or "M"
Changes in version 1.4.1 (2015-06-30)
-------------------------------------
IMPROVEMENTS
o correctBins() now filters out bins with missing loess correction estimate
Changes in version 1.4.0 (2015-04-17)
-------------------------------------
RELEASE
o Bioconductor 3.1
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