Changes in version 1.17
o BSseq() will no longer reorder inputs. Previously, the returned
_BSseq_ object was ordered by ordering the loci, although this
behaviour was not documented. BSseq() may still filter out loci
if rmZeroCov = FALSE or collapse loci if strandCollapse = FALSE
or duplicate loci are detected, but the relative order of loci
in the output will match that of the input.
o Fix bug with maxGap argument of BSmooth(). The bug meant that
the 'maximum gap between two methylation loci' was incorrectly
set to 2 * maxGap + 1 instead of maxGap. This likely did not
affect results for users who left the default value of maxGap =
10^8 but may have affected results for small values of maxGap.
o Cleaning up Imports and Suggests.
Changes in version 1.13
o 1.13.6: Fix performance regression in BSmooth(). Thanks to Shan
Andrews for the report (<URL:
https://github.com/kasperdanielhansen/bsseq/pull/57>).
o 1.13.5: Fix major bug in combine() and combineList(). *This
bug led to bad BSseq objects with incorrect methylation
estimates due to incorrect 'M', 'Cov', 'coef', and 'se.coef'
assays.* To be safe, BSseq objects created with versions 1.13.0
to 1.13.4 should be re-created using a newer version. More
specifically, any BSseq objects created with combine() or
combineList() should be re-created. Also, BSseq objects
created using read.bismark() or read.bsmooth() with multiple
'files' should be re-created. Thanks to Alejandro Reyes
(@areyesq89) for the report (<URL:
https://github.com/kasperdanielhansen/bsseq/pull/54>).
o 1.13.4: Fix performance regression in getMeth() and
getCoverage() when 'regions' were supplied. Thanks to Alejandro
Reyes (@areyesq89) for the report (<URL:
https://support.bioconductor.org/p/97611/>).
o Moved vignettes to Rmd.
Changes in version 1.11
o bsseq now uses DelayedMatrix objects from the DelayedArray
package for all matrix-like data. This enables large data to be
stored on disk rather than in memory.
o Serialized (saved) BSseq, BSseqTstat, and BSseqStat objects
will need to be updated by invoking x <- updateObject(x).
Changes in version 1.7
o Fixing an error with reading multiple samples aligned with
bismark in the format "cytosineReport".
Changes in version 1.5
o new function strandCollapse for collapsing forward and reverse
strand data to be unstranded.
o Updated read.bismark() to support the cytosine report files;
both formats are supported. Other minor updates (mostly
internal) to read.bismark(). Greatly improved documentation of
this function, paying particular attention to differences in
file formats between versions of Bismark.
Changes in version 0.11
o Converted to using Authors@R in the DESCRIPTION file.
o plotRegion did not respect the col/lty/lwd argument if given
explicitely as opposed to through pData(). Reported by Karen
Conneely <kconnee@emory.edu>.
o Fixed an issue introduced by the previous change (to
plotRegion). Reported (with a fix) by Tim Triche Jr
<tim.triche@gmail.com>.
o Fixed a serious bug in collapseBSseq reported by Julien Roux
<jroux@uchicago.edu>: it would use the Meth values instead of
Cov for the final object's Cov. However, this will result in
the return object having a methylation of 100 percent across
all loci, so hopefully users will have seen this for
themselves.
o Fixed a bug in combineList which made combineList use "slow"
code even in a special case where a faster shortcut was
possible. This bug fix does not change the output of the
function under any input, it only makes it faster. Reported by
Julien Roux <jroux@uchicago.edu>.
o validity now checks for the presence of colnames (sampleNames)
which was assumed to be set. Reported by Kevin Rue-Albrecht
<kevin.rue@ucdconnect.ie>.
o Fixed a man page issue.
o Slightly changed CITATION.
o Added GitHub URL to DESCRIPTION.
Changes in version 0.9
o Fixed a problem with "width" in the title of bsseq plots.
o plot.BSseqTstat now allows for BSseqTstat objects computed
without correction.
o validObject(BSseq) has been extended to also check for
sampleNames consistency.
o Fixed a bug related to validity checking.
o Increased maxk from 10,000 to 50,000 in calls to locfit, to
allowing fitting the model on genomes with unusally long
chromosomes (Thanks to Brian Herb for reporting).
o The class representation for class 'BSseq' has changed
completely. The new class is build on 'SummarizedExperiment'
from GenomicRanges instead of 'hasGRanges'. Use 'x <-
updateObject(x)' to update serialized (saved) objects.
o Fixing a problem in orderBSseq related to chromosome names.
o Allowed user specification of maxk, with a default of 10,000 in
BSmooth.
o Many bugfixes made necessary by the new class representation.
o Better argument checking in BSmooth.tstat.
o A few undocumented functions are now documented.
o Rewrote orderBSseq
Changes in version 0.7
o Removed the returnRaw argument to read.bismark() as it was
unnecessary (Bismark output files does not have additional
information beyond M and Cov and genomic positions, unlike
BSmooth).
o Moved the Bismark example data from data to inst/extdata.
o combineList() now deals with the case where the list of BSseq
objects have different genomic locations. This speeds up
read.bismark() substantially.
o Exposed combineList() as a faster alternative to
Reduce(combine, list).
o Updated the code for the plotting routines (plotRegion). This
should not have an impact on user-visible code.
o Added read.bismark() function to parse output from the Bismark
alignment suit [thanks to Pete Hickey].
o Refactorized plotting code.
Changes in version 0.6
o Fixed a bug in getMeth, where type="raw" resulted in an error
for non-smoothed data objects.
o Updated CITATION and citations in the vignettes.
o Now read.bsmooth supports both gzipped and non-gzipped files,
whereas previously it assumed the output files to be gzipped.
Thanks to Andreas Schoenegger for reporting this problem.
o Fixed a bug in combine() that also resulted in a bug in
read.bsmooth when multiple input directories were specified.
Bug reported by Andreas Schoenegger.
Changes in version 0.4
o Improved combine and fixed a bug. Also added a non-exported
combineList for testing.
o Bug fix to read.bsmooth; it now works correctly for the default
settings (= returning a single object of class BSseq and not a
list).
o Getting ready for initial release on Bioconductor.
o Updated the citations in the vignette(s) and the CITATION file.