NEWS

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ACE 1.9.3 (2021-01-28)

• Now defaulting to exclude sex chromosomes from model fitting
• Also included sgc argument in twosamplecompare
• Data frame output of ACEcall and twosamplecompare are now restricted to selected chromosomes

ACE 1.9.1 (2021-01-15)

• accommodating fitting of chromosomes with only a single germline copy (e.g. X and Y in males)
• added the option to specify which cellularities to include in squaremodel
• option to save readCounts-object in runACE

ACE 1.5.2 (2020-04-14)

• updated maintainer e-mail address

ACE 1.5.1 (2020-01-14)

• fixed a bug in getadjustedsegments that joined adjacent chromosomes with same segment values

ACE 1.1.2 (2019-04-23)

• added citation information!
• fixed bug in getadjustedsegments and twosamplecompare with non-matching NAs

ACE 1.1.1 (2018-11-13)

• added forcesegmentsontemplate function
• speed boost by small coding change in model fitting
• added argument in loopsquaremodel to make returning the models optional and flexible (see documentation)

ACE 0.99.6 (2018-07-26)

• bugfix in linkvariants: no default freqindex

ACE 0.99.4 (2018-06-26)

IMPROVEMENTS

• changed linkmutationdata to linkvariants
• linkvariants can estimate copies of heterozygous germline variants
• linkvariants calculates the upper and lower bound of a given confidence level when read depth is given
• changed postanalysisloop to accommodate linkvariants
• added argument in runACE to specify genome build
• several minor documentation amendments
• improved coding robustness using seq and seq_along functions

ACE 0.99.0 (2018-05-24)

SUBMISSION

• initial submission to Bioconductor