exportBins(..., format = "vcf")did not add meta-data information for fieldENDto the VCF file header.
poolRuns()would give an error "Error in colMeans2(oldphenodata, cols = numericCols, useNames = FALSE) : Argument 'x' must be a matrix or a vector."
-
Fix markup typo in
help("exportBins"). -
Add package test for
poolRuns().
- The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.19 for R (>= 4.4.0).
- The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.18 for R (>= 4.3.1).
- The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.17 for R (>= 4.3.0).
- The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.16 for R (>= 4.2.2).
- Now the package gives an informative error message when an outdated version of the future package is used. It requires future (>= 1.22.1).
- A few functions used
class(x) == "data.frame"rather thaninherits(x, "data.frame").
- The version number was bumped for the Bioconductor devel version, which is now Bioconductor 3.16 for R-devel.
- The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.15 for R (>= 4.2.0).
- The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.15 for R-devel.
- The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.14 for R (>= 4.1.1).
segmentBins()would report the sample names as"NA"in output messages if the sample name contained hyphens, or other symbols automatically replaced bydata.frame(..., check.names = TRUE). This was a harmless bug.
- All internal row and column-based matrixStats calls now avoid overhead from handling row and column names.
- Moved future from Imports to Suggests.
- Vignette now illustrate parallelization using the
multisessionfuture strategy, instead of the deprecatedmultiprocessstrategy.
- Argument
seedsofsegmentBins()is defunct. It has been deprecated and ignored since QDNAseq 1.21.3 (September 2019).
-
Now argument
logTransformofexportBins()is ignored iftype = "calls". -
Now
exportBins()returns the pathname to the files written.
-
Test code coverage was increased from 42% to 52%.
-
Add package test for
exportBins().
-
exportBins(fit, format = "seg", ...)andformat = "vcf"would merge segments with equal copy-number calls if they were interweaved with copy-neutral segments. -
exportBins(fit, format = "seg", ...)andformat = "vcf"produced an obscure error with messagesError in dimnames(x) <- dn : length of dimnames [2] not equal to array extentfor samples with no copy-number abberations. -
exportBins(fit, format = "seg", file = ...)andformat = "vcf"did not respect argumentfilebut instead wrote files of its own names to the current working directory. -
exportBins()would corrupt optionscipen. Now it is left unchanged.
callBins()produces warnings onRecycling array of length 1 in vector- array arithmetic is deprecated. Use c() or as.vector() instead.in R (>= 3.4.0). This is a problem in the package CGHcall dependency and is something that needs to be fixed there. For further details, please see tgac-vumc/CGHcall#2.
-
Test code coverage was increased from 32% to 39%.
-
Added package tests for
binReadCounts().
binReadCounts()would fail when specifying argumentchunkSize. The fix was to require future package version 1.22.1 or newer.
- Add package test for
binReadCounts().
- The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.13 for R (>= 4.0.3).
- The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.12 for R (>= 4.0.0).
- The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.11 for R (>= 3.6.1).
- Bioconductor 3.10
- Link to the 'GEM library' tool was broken.
plot(...,logTransform=TRUE, doSegments=TRUE)on QDNAseqSignals would position segments that were out of range incorrectly, because it forgot to take the log transform on those outliers.
- Bin annotation data files are no longer downloaded automatically. They are instead part of Bioconductor annotation packages QDNAseq.hg19 and QDNAseq.mm10, which needs to be installed by the user. If not installed, an error is now produced. The reason for this change, is that the QDNAseq maintainers will no longer host QDNAseq bin annotation files online (in the cloud).
- All functions that produce verbose output gained argument
verbose. For backward compatibility, it currently defaults to 'verbose=TRUE'but that may be changed to 'verbose=FALSE'in a future release.
-
callBins()now respects optionQDNAseq::verbosefor controlling whether output from the CGHcall package should be relayed or not. -
MEMORY: Utilize more memory-efficient matrixStats functions
colSums2(),colMeans2(), etc.
- Argument
seedsofsegmentBins()is deprecated because it did not use proper parallel random number generation (RNG). We now instead rely onfuture.apply::future_lapply(..., future.seed=TRUE)for this.
-
Package now imports the future and future.apply packages; previously the future was listed as a suggested package.
-
Package no longer depends on BiocParallel.
-
binReadCounts()now uses the future framework instead of BiocParallel for parallelization.
- MEMORY: Avoiding data type coercions in more places by for instance making sure that vectors and matrices are initated with the values of the correct data type (instead of the default NA, which is a logical value).
-
Using
future_lapply()andfuture_apply()of the well-tested future.apply package instead of internal analogue implementations. -
TESTS: Now testing numerical reproducibility also for parallel processing (using future strategies
multisessionandmulticore). -
TESTS: Now asserting numerical reproducibility of also
segmentBins()andcallBins().
exportVCF()is no longer exported. UseexportBins(..., format="vcf")instead.
- Bioconductor 3.9.
- Bioconductor 3.8.
- Bioconductor 3.7.
- Bioconductor 3.6.
- Bioconductor 3.5.
-
VCF and SEG file export have been implemented to allow use of downstream analysis tools such as Cartegenia (NGS) Bench.
-
binReadCounts()now supports parallel computing. -
calculateBlackListByRegions()has been implemented for convient bin overlap calculation of any set of regions.
- Bioconductor 3.4.
- Bioconductor 3.3.
-
estimateCorrection(),segmentBins(),createBins(), andcalculateBlacklist()now support parallel computing (see vignette for more details) -
callBins()can now also use cutoffs instead of CGHcall. -
binReadCounts()now contains parameterpairedEndsto specify when using paired-end data, so that expected variance can be calculated correctly -
segmentBins()now allows seeds for random number generation to be specified for reproducibility. -
binReadCounts()supports chunked processing of BAM files. -
estimateCorrection()now also allows correcting for only GC content or mappability.
-
applyFilters()andhighlightFilters()now work properly when using a numerical value for parameter residual. -
highlightFilters()no longer highlights entire chromosomes for which the residual filter is missing altogether, which matches the behavior ofapplyFilters(). -
getBinAnnotations()now allows custom bin annotations to be loaded via the path parameter even when an annotation package has been installed. -
phenodata files with a single variable are now handled correctly.
-
calculateMappability()now retains correct chromosome order even whenbigWigAverageOverBedreorders them. -
calculateBlacklist()now correctly handles non-integer chromosome names.
- Bioconductor 3.2.
chromosomes()no longer tries to return chromosome names as an integer vector, but returns a character vector instead.
plot()andcalculateMappability()now work also for other chromosome names besides numbers and"X","Y", and"MT".
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".
correctBins()now filters out bins with missing loess correction estimate.
- Bioconductor 3.1.
- Update package maintainer.
createBins()now also works for species not supported by GenomeInfoDb (such as Canis lupus familiaris).
applyFilters()now ignores the residual filter for chromosomes for which it does not exist (instead of always filtering out the entire chromosome).
-
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).
-
Clarify the use of log2/sqrt transformation in
segmentBins().
- Bioconductor 3.0.
-
segmentBins()supports another transformation option besides log2:sqrt(x + 3/8), which stabilizes the variance. -
plot()can skip plotting of segments and calls by specifyingdoSegments=FALSEanddoCalls=FALSE. -
exportBins()also supports BED files.
exportBins()saves base pair positions in fixed notation instead of scientific.
- Gix 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.
getBinAnnotations()fixed after being broken by a change in Bitbucket.
-
Added
exportBins()for exporting to a file. -
Switch graphics in the vignette to PNG.
-
plot()honors user-specified values forxlabandxaxt. -
plot()allows omission of labels for the standard deviation and the number of data points. -
Improve diagnostic messages.
smoothOutlierBins()correctly ignores bins filtered out.
- Initial release as part of Bioconductor 2.14.