Changes in version 1.9.3 (2021-01-28) ------------------------------------- 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) ------------------------------------- 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) ------------------------------------- o updated maintainer e-mail address Changes in version 1.5.1 (2020-01-14) ------------------------------------- o fixed a bug in getadjustedsegments that joined adjacent chromosomes with same segment values Changes in version 1.1.2 (2019-04-23) ------------------------------------- o added citation information! o fixed bug in getadjustedsegments and twosamplecompare with non-matching NAs Changes in version 1.1.1 (2018-11-13) ------------------------------------- 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) ------------------------------------- o bugfix in linkvariants: no default freqindex Changes in version 0.99.4 (2018-06-26) ------------------------------------- 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