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NEWS
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NEWS
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Changes in version 1.9.3 (2021-01-28)
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o Now defaulting to exclude sex chromosomes from model fitting
o Also included sgc argument in twosamplecompare
o Data frame output of ACEcall and twosamplecompare are now restricted to selected chromosomes
Changes in version 1.9.1 (2021-01-15)
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o accommodating fitting of chromosomes with only a single germline copy (e.g. X and Y in males)
o added the option to specify which cellularities to include in squaremodel
o option to save readCounts-object in runACE
Changes in version 1.5.2 (2020-04-14)
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o updated maintainer e-mail address
Changes in version 1.5.1 (2020-01-14)
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o fixed a bug in getadjustedsegments that joined adjacent chromosomes with same segment values
Changes in version 1.1.2 (2019-04-23)
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o added citation information!
o fixed bug in getadjustedsegments and twosamplecompare with non-matching NAs
Changes in version 1.1.1 (2018-11-13)
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o added forcesegmentsontemplate function
o speed boost by small coding change in model fitting
o added argument in loopsquaremodel to make returning the models optional and flexible (see documentation)
Changes in version 0.99.6 (2018-07-26)
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o bugfix in linkvariants: no default freqindex
Changes in version 0.99.4 (2018-06-26)
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IMPROVEMENTS
o changed linkmutationdata to linkvariants
o linkvariants can estimate copies of heterozygous germline variants
o linkvariants calculates the upper and lower bound of a given confidence level when read depth is given
o changed postanalysisloop to accommodate linkvariants
o added argument in runACE to specify genome build
o several minor documentation amendments
o improved coding robustness using seq and seq_along functions
Changes in version 0.99.0 (2018-05-24)
-------------------------------------
SUBMISSION
o initial submission to Bioconductor