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KLINK 1.1.0

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@magnusdv magnusdv released this 12 May 11:39
v1.1.0
48d4470

New features

  • Added new datasets sibship and halfsib. In the app, these are available as Example1 and Example2, respectively.

  • The default genetic map, previously built-in to KLINK, has been moved to the norSTR package under the name map50, and is now imported from there.

  • KLINK now employs the special lumping methods recently implemented in pedprobr and pedmut. This permits the use of complex mutation models (e.g. Stepwise) in most common pedigrees, including paternity and full/half siblings. In larger pedigrees, nonlumpable models are replaced with the simpler 'Equal' model.

  • The LR table shown in the app has a new look, now using the same layout and marker order as the other tables.
    The "LR table" sheet of the Excel download also uses this marker order.
    Note: The Report sheets has not changed.

  • New app controls Empty markers (hide/show) and Likelihoods (hide/show/loglik) for the LR table in the app and the Excel download.

  • New app control Decimals for setting the number of decimals in displayed tables.

  • Inconsistent marker names are handled more gracefully. For instance, Penta D, Penta.D, PentaD, PENTA D are now recognised as the same marker (similarly for other markers, notably Penta E and vWA).

  • The Marker data table now excludes unused mutation model columns (app only).

  • The Excel download includes a new sheet, Plots, containing the two pedigree plots.

  • Added tooltips explaining app controls and table columns.

  • Busy-indicator: A pulsating effect is now shown when the app is busy.

  • Renamed columns in the linkage map: Chrom -> Chr and PosCM -> cM. When loading custom maps, variations of these names are accepted.

  • Only on shinyapp.io: Show banner warning about uploading sensitive data.

Minor changes and fixes

  • Empty the .xml field when a new .fam file is loaded.

  • RStudio now stops the app when the user closes the browser.

  • Graceful handling of input without data.

  • The Marker map control has been moved up to the Input app region.

  • Fixed a bug appearing when the input file contains an unmapped single marker.

  • Fixed a bug giving slightly incorrect LR values in some cases when a stepwise mutation model was used. This bug was related to lumping, which is now handled differently (see entry under New features).

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