Improved Allele-Specific Copy Number of SNP Microarrays for Downstream Segmentation

A multi-array post-processing method of allele-specific copy-number estimates (ASCNs).


Package: calmate

Version: 0.12.1 [2015-10-26] o ROBUSTNESS: Explicitly importing core R functions. o Package now requires R (>= 3.1.1) released July 2014. This allows us to use BioC (>= 3.0) (October 2014).

Version: 0.12.0 [2015-02-23] o ROBUSTNESS: Package test coverage is 32%. o ROBUSTNESS: Added missing import. o Updated package dependencies.

Version: 0.11.2 [2014-01-30] o Updated package dependencies.

Version: 0.11.1 [2013-10-17] o Updated the reference to the CalMaTe paper.

Version: 0.11.0 [2013-10-17] o ROBUSTNESS: Now importing only what needs to be imported and formally declaring all S3 methods in NAMESPACE. o Package now requires R (>= 2.15.0) [and Bioc (>= 2.10.0)]. o Updated package dependencies.

Version: 0.10.3 [2013-09-21] o CLEANUP: Now only using '[email protected]' in DESCRIPTION, which is possible since R (>= 2.14.0). o Updated package dependencies.

Version: 0.10.2 [2013-08-03] o 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. o Forgot to import rowAlls() from 'matrixStats'. o Added an [email protected] field to DESCRIPTION. o Updated package dependencies.

Version: 0.10.1 [2013-05-22] o CRAN POLICY: Now all Rd \usage{} lines are at most 90 characters long. o Updated package dependencies.

Version: 0.10.0 [2013-01-05] o Updated package dependencies. o Now CalMaTeCalibration implements ParametersInterface. o ROBUSTNESS: Now package declares S3 methods in the namespace. o CLEANUP: Now packages MASS, matrixStats, R.methodsS3 and R.oo are only imported (not loaded/attached). o BUG FIX: 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.

Version: 0.9.3 [2012-04-24] o Updated package dependencies. o Updated references to the CalMaTe manuscript.

Version: 0.9.2 [2012-03-18] o Updated help("calmate").

Version: 0.9.1 [2012-02-23] o Now package explicitly imports 'utils' and no longer relies on 'R.oo' and/or 'R.utils' for loading 'utils'.

Version: 0.9.0 [2012-02-21] o UPDATE: 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).

Version: 0.8.1 [2012-02-19] o Made findUnitsTodo() for CalMaTeCalibration smarter. Before it would detect all non-polymorphic loci as non-fitted.

Version: 0.8.0 [2012-02-19] o 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. o SPEEDUP: the internal CalMaTe fit function is now called directly, which avoids the method dispatch overhead that otherwise applies to each SNP fitted. o ROBUSTNESS: Added system tests to test all flavors of the fitting algorithms.

Version: 0.7.4 [2012-02-06] o Now additional arguments '...' of CalMaTeCalibration(...) are passed to calmateByTotalAndFracB() by process(). This makes it possible to specify all tuning parameters of the CalMaTe method. o DEPRECATED: Now argument 'references' of process() is obsolete and gives an error. Specify it via CalMaTeCalibration() instead.

Version: 0.7.3 [2012-01-31] o Updated package dependencies. o BUG FIX: 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.

Version: 0.7.2 [2011-11-15] o ROBUSTNESS: Improved validation of argument 'references' to CalMaTeCalibration(), calmateByTotalAndFracB(), and calmateByThetaAB(). o DOCUMENTATION: Added a section 'Reference samples' to the help of CalMaTeCalibration. o DEPRECATED: Argument 'references' of process() of CalMaTeCalibration is deprecated. Instead, pass it to CalMaTeCalibration(). o ROBUSTNESS/BUG FIX: 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.

Version: 0.7.1 [2011-11-30] o DOCUMENTATION: Updated links on help pages. o Updated package dependencies.

Version: 0.7.0 [2011-10-24] o Added a NAMESPACE.

Version: 0.6.7 [2011-09-16] o Added missing authors to the DESCRIPTION.

Version: 0.6.6 [2011-08-01] o Added some more test scripts. o 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').

Version: 0.6.5 [2011-03-18] o BUG FIX: calmateByTotalAndFracB() required that the 2nd dimension of argument 'data' had names "total" and "fracB". Likewise, calmateByThetaAB() required that they were "A" and "B".

Version: 0.6.4 [2011-03-12] o GENERALIZATION: Now allocateOutputDataSets() for CalMaTeCalibration no longer requires write permissions if the data set already exists. o Added argument 'references' to the CalMaTeCalibration constructor. o 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/.

Version: 0.6.3 [2010-11-02] o Updated the help page for the package itself.

Version: 0.6.2 [2010-09-28] o Updated the example for the CalMaTeCalibration help page to illustrate how to extract the total copy numbers correctly.

Version: 0.6.1 [2010-08-05] o ROBUSTNESS: Now calmateByThetaAB() and calmateByTotalAndFracB() asserts that there are at least two samples. o BUG FIX: calmateByTotalAndFracB() assumed that there where enough units and samples so that subsetting would not drop singleton dimension. Now we use drop=FALSE everywhere. o BUG FIX: calmateByThetaAB() would not work if there was only one unit.

Version: 0.6.0 [2010-08-02] o 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.

Version: 0.5.2 [2010-08-02] o CLEANUP: Dropped obsolete internal calmate() and refineCN() functions.

Version: 0.5.1 [2010-07-31] o BUG FIX: process() for CalMaTeCalibration would only run one chunk.

Version: 0.5.0 [2010-07-30] o Renamed CalMaTeNormalization to CalMaTeCalibration.

Version: 0.4.2 [2010-07-22] o BUG FIX: Now process() for CalMaTeNormalization returns immediately if there are no units left.

Version: 0.4.1 [2010-06-29] o Added support for process(..., force=TRUE) in CalMaTeNormalization.

Version: 0.4.0 [2010-06-21] o Added an early version (really!) of CalMaTeNormalization. It still does not store parameter estimates; only the normalized signals.

Version: 0.3.1 [2010-06-19] o Now the default CalMaTe method is no longer truncating negative ASCN signals. o 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.

Version: 0.3.0 [2010-06-18] o CLEAN UP: 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.

Version: 0.2.2 [2010-06-18] o BUG FIX: Now "truncating" by x[x < eps] <- eps (was x[x == 0] <- eps). o BUG FIX: A few potential bugs where removed. o CLEAN UP: Tidied up the code. o CLEAN UP: Removed obsolete files.

Version: 0.2.1 [2010-05-19] o Added weightedCalMaTeByThetaAB() and weightedCalMaTeByTotalAndFracB(). The former replaces weightedCalMaTeByASCN(). o Added internal thetaAB2TotalAndFracB() and totalAndFracB2ThetaAB(). o Decreased the package dependencies. Now aroma.core is only suggested, but not required.

Version: 0.2.0 [2010-05-18] o 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.

Version: 0.1.2 [2010-05-18] o CLEAN UP: Source code cleanup and standardization. o ROBUSTNESS: Added a redundancy test.

Version: 0.1.1 [2010-05-04]

Version: 0.1.0 [2010-05-04] o Made into an R package.

Version: 0.0.1 [2010-05-03] o Created.

Reference manual

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0.12.1 by Henrik Bengtsson, 6 years ago

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Browse source code at

Authors: Maria Ortiz [aut, ctb] , Ander Aramburu [ctb] , Henrik Bengtsson [aut, cre, cph] , Pierre Neuvial [aut, ctb] , Angel Rubio [aut, ctb]

Documentation:   PDF Manual  

LGPL (>= 2.1) license

Imports utils, MASS, R.methodsS3, R.oo, matrixStats, R.filesets

Depends on R.utils, aroma.core

Suggests DNAcopy

See at CRAN