NEWS

calmate 0.13.0 (2022-03-08)

NEW FEATURES

Setting option 'calmate.troubleshoot' to TRUE will result in an object '.calmate.troubleshoot' useful for troubleshooting being saved to the global environment if and only if qr.solve() produces an error, e.g. singular matrix 'a' in solve.

SOFTWARE QUALITY

Package now requires R (>= 3.2.1) because of aroma.core.
Updated package dependencies.
SPEEDUP: Utilizing subsetted matrixStats (>= 0.50.0) calculations.
Package test coverage is 49% (was 32%).

DOCUMENTATION

Add CITATION file.

BUG FIXES

calmateByThetaAB() and calmateByTotalAndFracB() generated a "too few arguments" error when they tried to generate another error.

calmate 0.12.1 (2015-10-27)

SIGNIFICANT CHANGES

Package now requires R (>= 3.1.1) released July 2014. This allows us to use Bioconductor (>= 3.0) (October 2014).

SOFTWARE QUALITY

Explicitly importing core R functions.

calmate 0.12.0 (2015-02-23)

SOFTWARE QUALITY

Package test coverage is 32%.
Updated package dependencies.

BUG FIXES

Added missing import.

calmate 0.11.2

SOFTWARE QUALITY

Updated package dependencies.

calmate 0.11.1

DOCUMENTATION

Updated the reference to the CalMaTe paper.

calmate 0.11.0 (2013-10-17)

SIGNIFICANT CHANGES

Package now requires R (>= 2.15.0) [and Bioc (>= 2.10.0)].

SOFTWARE QUALITY

Now importing only what needs to be imported and formally declaring all S3 methods in NAMESPACE.
Updated package dependencies.

calmate 0.10.3

SOFTWARE QUALITY

Now using only 'Authors@R' in DESCRIPTION available since R (>= 2.14.0).
Updated package dependencies.

calmate 0.10.2 (2013-08-04)

SOFTWARE QUALITY

Updated examples and system tests to use matrixStats::rowMedians() so that they work with aroma.core (>= 2.10.0) without having to load the 'matrixStats' package.
Added an Authors@R field to DESCRIPTION.
Updated package dependencies.

BUG FIXES

Forgot to import rowAlls() from 'matrixStats'.

calmate 0.10.1

CRAN POLICY

Now all Rd \usage{} lines are at most 90 characters long.

SOFTWARE QUALITY

Updated package dependencies.

calmate 0.10.0 (2013-01-08)

NEW FEATURES

Now CalMaTeCalibration implements ParametersInterface.

SOFTWARE QUALITY

Updated package dependencies.
Now package declares S3 methods in the namespace.
CLEANUP: Now packages MASS, matrixStats, R.methodsS3 and R.oo are only imported (not loaded/attached).

BUG FIXES

Previous version was not compatible with R.filesets 1.9.0 and aroma.core 2.8.0 resulting in "Error: 'sapply' is not an exported object from 'namespace:R.filesets'". Thanks to Zheng Siyuan (MD Anderson) for reporting on this.

calmate 0.9.3

NEW FEATURES

Updated package dependencies.

DOCUMENTATION

Updated references to the CalMaTe manuscript.

calmate 0.9.2 (2012-03-19)

DOCUMENTATION

Updated help("calmate").

calmate 0.9.1

SOFTWARE QUALITY

Now package explicitly imports 'utils' and no longer relies on 'R.oo' and/or 'R.utils' for loading 'utils'.

calmate 0.9.0

SIGNIFICANT CHANGES

CalMaTe algorithm v2 is being finalized. Main updates are: (a) The estimation of the model parameters are now done solely based on reference samples. In previous versions, some of the initial estimation steps were using also non-reference samples. (b) For a small number of SNPs, the main CalMaTe scheme for estimating parameters would not converge or converge poorly. For such SNPs, CalMaTe now falls back to using a median-based estimator. For more details, see help(fitCalMaTeInternal).

calmate 0.8.1

SIGNIFICANT CHANGES

Made findUnitsTodo() for CalMaTeCalibration smarter. Before it would detect all non-polymorphic loci as non-fitted.

calmate 0.8.0

NEW FEATURES

BACKWARD COMPATIBILITY: Added argument 'flavor' to calmateByThetaAB() and CalMaTeCalibration so that it is possible use previous versions of CalMaTe model estimators. The flavor is now reflected in the "asterisk" (the default) tags of CalMaTeCalibration.

SOFTWARE QUALITY

SPEEDUP: The internal CalMaTe fit function is now called directly, which avoids the method dispatch overhead that otherwise applies to each SNP fitted.
ROBUSTNESS: Added system tests to test all flavors of the fitting algorithms.

calmate 0.7.4

NEW FEATURES

Now additional arguments '...' of CalMaTeCalibration(...) are passed to calmateByTotalAndFracB() by process(). This makes it possible to specify all tuning parameters of the CalMaTe method.

DEPRECATED AND DEFUNCT

Now argument 'references' of process() is obsolete and gives an error. Specify it via CalMaTeCalibration() instead.

calmate 0.7.3

Updated package dependencies. BUG FIXES:
The bug fix in v0.7.2 for handling the special case where a SNP has the same genotype in all samples introduced another bug giving incorrect results in that special case.

calmate 0.7.2

NEW FEATURES

ROBUSTNESS: Improved validation of argument 'references' to CalMaTeCalibration(), calmateByTotalAndFracB(), and calmateByThetaAB().

DOCUMENTATION

Added a section 'Reference samples' to the help of CalMaTeCalibration.

DEPRECATED AND DEFUNCT

Argument 'references' of process() of CalMaTeCalibration is deprecated. Instead, pass it to CalMaTeCalibration().

BUG FIXES

If in some SNPs, the samples include only a single genotype (usually AA or BB), the genotype AA is interpreted as BB in half of the samples and vice verse (and the returned value is reversed again). There was a bug in the code that occurred iff all the reference samples have the same genotype and the number of reference samples is smaller than half of the total number of samples.

calmate 0.7.1

DOCUMENTATION

Updated links on help pages.

SOFTWARE QUALITY

Updated package dependencies.

calmate 0.7.0 (2011-10-25)

SOFTWARE QUALITY

Added a NAMESPACE.

calmate 0.6.7

SOFTWARE QUALITY

Added missing authors to the DESCRIPTION.

calmate 0.6.6 (2011-09-16)

SOFTWARE QUALITY

Added some more test scripts.
WORKAROUND: In order for the package to work with the most recent version of R devel, which automatically add namespaces to packages who do not have one, we explicitly have specify that this package should use, for instance, cat() of R.utils (instead of 'base').

calmate 0.6.5

BUG FIXES

calmateByTotalAndFracB() required that the 2nd dimension of argument 'data' had names "total" and "fracB". Likewise, calmateByThetaAB() required that they were "A" and "B".

calmate 0.6.4

NEW FEATURES

GENERALIZATION: allocateOutputDataSets() for CalMaTeCalibration no longer requires write permissions if the data set already exists.
Added argument 'references' to the CalMaTeCalibration constructor.
REPRODUCIBLE RESEARCH: Added scripts to process the data and generate the figures used in the CalMaTe manuscript(s). These scripts are available under testScripts/publications/.

calmate 0.6.3

DOCUMENTATION

Updated the help page for the package itself.

calmate 0.6.2

DOCUMENTATION

Updated the example for the CalMaTeCalibration help page to illustrate how to extract the total copy numbers correctly.

calmate 0.6.1

NEW FEATURES

Now calmateByThetaAB() and calmateByTotalAndFracB() asserts that there are at least two samples.

BUG FIXES

calmateByTotalAndFracB() assumed that there where enough units and samples so that subsetting would not drop singleton dimension. Now we use drop=FALSE everywhere.
calmateByThetaAB() would not work if there was only one unit.

calmate 0.6.0

NEW FEATURES

Added argument 'refAvgFcn' to calmateByTotalAndFracB() and calmateByThetaAB(). It is used to standardize the total copy number of both SNPs and non-polymorphic loci using the same estimator for the average reference signal.

calmate 0.5.2

DEPRECATED AND DEFUNCT

Dropped obsolete internal calmate() and refineCN() functions.

calmate 0.5.1

BUG FIXES

process() for CalMaTeCalibration would only run one chunk.

calmate 0.5.0

SIGNIFICANT CHANGES

Renamed CalMaTeNormalization to CalMaTeCalibration.

calmate 0.4.2

BUG FIXES

Now process() for CalMaTeNormalization returns immediately if there are no units left.

calmate 0.4.1

NEW FEATURES

Added support for process(..., force=TRUE) in CalMaTeNormalization.

calmate 0.4.0

NEW FEATURES

Added an early version (really!) of CalMaTeNormalization. It still does not store parameter estimates; only the normalized signals.

calmate 0.3.1

NEW FEATURES

Now the default CalMaTe method is no longer truncating negative ASCN signals.
Added argument 'truncate=FALSE' to internal calmateByThetaAB() and rewrote the code to do the truncation in (CA,CB) space. The truncation is done such that CA+CB is preserved.

calmate 0.3.0

SOFTWARE QUALITY

CLEANUP: Rewrote calmateByThetaAB() so it is no longer using old calmate() but a new internal fitCalMaTe(). The latter should probably we incorporated "inline" in calmateByThetaAB() to better make use of vectorization.

calmate 0.2.2

BUG FIXES

Now "truncating" by x[x < eps] <- eps (was x[x == 0] <- eps).
A few potential bugs where removed.

SOFTWARE QUALITY

CLEANUP: Tidied up the code.
CLEANUP: Removed obsolete files.

calmate 0.2.1

NEW FEATURES

Added weightedCalMaTeByThetaAB() and weightedCalMaTeByTotalAndFracB(). The former replaces weightedCalMaTeByASCN().

SOFTWARE QUALITY

Added internal thetaAB2TotalAndFracB() and totalAndFracB2ThetaAB().
Decreased the package dependencies. Now aroma.core is only suggested, but not required.

calmate 0.2.0

NEW FEATURES

Added weightedCalMaTeByASCN() which takes an Jx2xI array of allele-specific signals, where J is the number of SNPs, 2 is the number of alleles, and I is the number of samples.