NEWS

---

copynumber 2.0.0

New features

• Added mm39 genome build support.

Bug fixes

• addChromlines(), get.seglim(), and plotCircle() had minor bugs fixed; several error messages had incomplete or misspelled arguments.
• aspcf(..., return.est = TRUE) now returns named logR estimates.
• aspcf(), multipcf(), pcf(), plotAberration(), plotHeatmap(), subsetData(), subsetSegments(), and winsorize() no longer error on matrix input.
• getArms() no longer splits a chromosome into p/q arms using another chromosome's boundary.
• interpolate.pcf() no longer errors on a missing chromosome or single-row input.
• mm7, mm8, and mm9 cytoband data no longer drops chromosome 1's first band.
• multipcf() no longer errors on a chromosome arm with a single probe.
• selectSegments() now returns a list, not a bare data frame, for large nseg.

Development

• Converted function documentation to roxygen2.
• Converted the vignette from Sweave to R Markdown.
• Added a pkgdown website.
• Added a testthat test suite (previously no automated tests).

copynumber 1.41.0

Version-only bumps per Bioconductor release, except where noted.

• 1.41.0 — devel bump after Bioconductor 3.17 (2023-04-25); no further releases followed
• 1.40.0 — Bioconductor 3.17 (2023-04-25); final Bioconductor release
• 1.39.1 — marked Deprecated (unresponsive maintainer, invalid contact email)
• 1.38.0 — Bioconductor 3.16 (2022-11-01)
• 1.36.0 — Bioconductor 3.15 (2022-04-26)
• 1.34.0 — Bioconductor 3.14 (2021-10-26)
• 1.32.0 — Bioconductor 3.13 (2021-05-19)
• 1.30.0 — Bioconductor 3.12 (2020-10-27)
• 1.29.0 — devel bump after Bioconductor 3.11; parent of this fork's 1.29.0.9000 (2020-04-27)
• 1.28.0 — Bioconductor 3.11 (2020-04-27)
• 1.26.0 — Bioconductor 3.10 (2019-10-29)
• 1.24.0 — Bioconductor 3.9 (2019-05-02)
• 1.22.0 — Bioconductor 3.8 (2018-10-30)
• 1.20.0 — Bioconductor 3.7 (2018-04-30)
• 1.18.0 — Bioconductor 3.6 (2017-10-30)
• 1.16.0 — Bioconductor 3.5 (2017-04-24)
• 1.14.0 — Bioconductor 3.4 (2016-10-17)
• 1.12.0 — Bioconductor 3.3 (2016-05-03)
• 1.10.0 — Bioconductor 3.2 (2015-10-13)
• 1.8.0 — Bioconductor 3.1 (2015-04-16)
• 1.6.0 — Bioconductor 3.0 (2014-10-13)
• 1.4.0 — Bioconductor 2.14 (2014-04-11)
• 1.2.0 — Bioconductor 2.13 (2013-10-14)

copynumber 1.29.0.9000

• Added hg38 and mm10 genome build support.
• Set up continuous integration via GitHub Actions.

copynumber 1.1.1

• plotHeatmap() now uses different colors above and below zero, instead of assuming upper.lim/lower.lim are symmetrical.

copynumber 1.0.0

• Initial version bump for Bioconductor 2.12 (2013-04-03).

copynumber 0.99.1

• Package first submitted to Bioconductor (2013-03-29).