NEWS.md

In ccagc/QDNAseq: Quantitative DNA Sequencing for Chromosomal Aberrations

Version 1.41.3 [2024-07-24]

Miscellaneous

• exportBins(..., format = "vcf") did not add meta-data information for field END to the VCF file header.

Version 1.41.2 [2024-07-23]

Bug Fixes

• poolRuns() would give an error "Error in colMeans2(oldphenodata, cols = numericCols, useNames = FALSE) : Argument 'x' must be a matrix or a vector."

Version 1.41.1 [2024-07-20]

Miscellaneous

• Fix markup typo in help("exportBins").

• Add package test for poolRuns().

Version 1.40.0 [2024-05-01]

Release

• The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.19 for R (>= 4.4.0).

Version 1.38.0 [2023-10-25]

Release

• The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.18 for R (>= 4.3.1).

Version 1.36.0 [2023-04-26]

Release

• The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.17 for R (>= 4.3.0).

Version 1.34.0 [2022-11-01]

Release

• The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.16 for R (>= 4.2.2).

Version 1.33.1 [2022-04-27]

Miscellaneous

• Now the package gives an informative error message when an outdated version of the future package is used. It requires future (>= 1.22.1).

Bug Fixes

• A few functions used class(x) == "data.frame" rather than inherits(x, "data.frame").

Version 1.33.0 [2022-04-26]

Release

• The version number was bumped for the Bioconductor devel version, which is now Bioconductor 3.16 for R-devel.

Version 1.32.0 [2022-04-26]

Release

• The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.15 for R (>= 4.2.0).

Version 1.31.0 [2021-10-27]

Release

• The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.15 for R-devel.

Version 1.30.0 [2021-10-27]

Release

• The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.14 for R (>= 4.1.1).

Version 1.29.6 [2021-10-23]

Bug Fixes

• segmentBins() would report the sample names as "NA" in output messages if the sample name contained hyphens, or other symbols automatically replaced by data.frame(..., check.names = TRUE). This was a harmless bug.

Version 1.29.5 [2021-10-20]

Performance

• All internal row and column-based matrixStats calls now avoid overhead from handling row and column names.

Miscellaneous

• Moved future from Imports to Suggests.

Version 1.29.4 [2021-10-16]

Documentation

• Vignette now illustrate parallelization using the multisession future strategy, instead of the deprecated multiprocess strategy.

Deprecation and Defunct

• Argument seeds of segmentBins() is defunct. It has been deprecated and ignored since QDNAseq 1.21.3 (September 2019).

Version 1.29.3 [2021-10-04]

New Features

• Now argument logTransform of exportBins() is ignored if type = "calls".

• Now exportBins() returns the pathname to the files written.

Software Quality

• Test code coverage was increased from 42% to 52%.

• Add package test for exportBins().

Bug Fixes

• exportBins(fit, format = "seg", ...) and format = "vcf" would merge segments with equal copy-number calls if they were interweaved with copy-neutral segments.

• exportBins(fit, format = "seg", ...) and format = "vcf" produced an obscure error with messages Error in dimnames(x) <- dn : length of dimnames [2] not equal to array extent for samples with no copy-number abberations.

• exportBins(fit, format = "seg", file = ...) and format = "vcf" did not respect argument file but instead wrote files of its own names to the current working directory.

• exportBins() would corrupt option scipen. Now it is left unchanged.

Known Issues

• callBins() produces warnings on Recycling 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 https://github.com/tgac-vumc/CGHcall/issues/2.

Version 1.29.2 [2021-09-22]

Software Quality

• Test code coverage was increased from 32% to 39%.

• Added package tests for binReadCounts().

Bug Fixes

• binReadCounts() would fail when specifying argument chunkSize. The fix was to require future package version 1.22.1 or newer.

Version 1.29.1 [2021-08-26]

Software Quality

• Add package test for binReadCounts().

Version 1.28.0 [2021-05-19]

Release

• The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.13 for R (>= 4.0.3).

Version 1.26.0 [2020-10-28]

Release

• The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.12 for R (>= 4.0.0).

Version 1.24.0 [2019-10-30]

Release

• The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.11 for R (>= 3.6.1).

Version 1.22.0 [2018-10-30]

Release

• Bioconductor 3.10

Version 1.21.6 [2019-09-25]

Bug Fixes

• Link to the 'GEM library' tool was broken.

Version 1.21.5 [2019-09-09]

Bug Fixes

• 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.

Version 1.21.4 [2019-09-06]

Significant Changes

• 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).

Version 1.21.3 [2019-09-04]

New Features

• 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.

Improvements

• callBins() now respects option QDNAseq::verbose for controlling whether output from the CGHcall package should be relayed or not.

• MEMORY: Utilize more memory-efficient matrixStats functions colSums2(), colMeans2(), etc.

Deprecation and Defunct

• Argument seeds of segmentBins() is deprecated because it did not use proper parallel random number generation (RNG). We now instead rely on future.apply::future_lapply(..., future.seed=TRUE) for this.

Version 1.21.2 [2019-09-03]

Significant Changes

• 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.

Improvements

• 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).

Software Quality

• Using future_lapply() and future_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 multisession and multicore).

• TESTS: Now asserting numerical reproducibility of also segmentBins() and callBins().

Version 1.21.1 [2019-08-30]

Significant Changes

• exportVCF() is no longer exported. Use exportBins(..., format="vcf") instead.

Version 1.20.0 [2019-05-02]

Release

• Bioconductor 3.9.

Version 1.18.0 [2018-10-30]

Release

• Bioconductor 3.8.

Version 1.16.0 [2018-04-30]

Release

• Bioconductor 3.7.

Version 1.14.0 [2017-10-30]

Release

• Bioconductor 3.6.

Version 1.12.0 [2017-04-23]

Release

• Bioconductor 3.5.

Improvements

• 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.

Version 1.10.0 [2016-10-18]

Release

• Bioconductor 3.4.

Version 1.8.0 [2016-05-04]

Release

• Bioconductor 3.3.

Improvements

• estimateCorrection(), segmentBins(), createBins(), and calculateBlacklist() now support parallel computing (see vignette for more details)

• callBins() can now also use cutoffs instead of CGHcall.

• binReadCounts() now contains parameter pairedEnds to 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.

Bug Fixes

• applyFilters() and highlightFilters() 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 of applyFilters().

• 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 when bigWigAverageOverBed reorders them.

• calculateBlacklist() now correctly handles non-integer chromosome names.

Version 1.6.0 [2015-10-14]

Release

• Bioconductor 3.2.

Improvements

• chromosomes() no longer tries to return chromosome names as an integer vector, but returns a character vector instead.

Bug Fixes

• plot() and calculateMappability() now work also for other chromosome names besides numbers and "X", "Y", and "MT".

Version 1.4.2 [2015-08-20]

Bug Fixes

• 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".

Version 1.4.1 [2015-06-30]

Improvements

• correctBins() now filters out bins with missing loess correction estimate.

Version 1.4.0 [2015-04-17]

Release

• Bioconductor 3.1.

Version 1.2.4 [2015-01-21]

Other

• Update package maintainer.

Version 1.2.3 [2015-01-20]

Bug Fixes

• createBins() now also works for species not supported by GenomeInfoDb (such as Canis lupus familiaris).

Version 1.2.2 [2014-12-23]

Improvements

• applyFilters() now ignores the residual filter for chromosomes for which it does not exist (instead of always filtering out the entire chromosome).

Version 1.2.1 [2014-11-01]

Improvements

• 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().

Version 1.2.0 [2014-10-14]

Release

• Bioconductor 3.0.

Improvements

• segmentBins() supports another transformation option besides log2: sqrt(x + 3/8), which stabilizes the variance.

• plot() can skip plotting of segments and calls by specifying doSegments=FALSE and doCalls=FALSE.

• exportBins() also supports BED files.

Bug Fixes

• exportBins() saves base pair positions in fixed notation instead of scientific.

Version 1.0.5 [2014-06-13]

Bug Fixes

• 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.

Version 1.0.4 [2014-05-23]

Bug Fixes

• getBinAnnotations() fixed after being broken by a change in Bitbucket.

Version 1.0.3 [2014-05-23]

Improvements

• Added exportBins() for exporting to a file.

• Switch graphics in the vignette to PNG.

Version 1.0.2 [2014-05-15]

Improvements

• plot() honors user-specified values for xlab and xaxt.

• plot() allows omission of labels for the standard deviation and the number of data points.

• Improve diagnostic messages.

Version 1.0.1 [2014-04-17]

Bug Fixes

• smoothOutlierBins() correctly ignores bins filtered out.

Version 1.0.0 [2014-04-14]

Release

• Initial release as part of Bioconductor 2.14.

ccagc/QDNAseq documentation built on July 28, 2024, 3:46 p.m.