R/qtl2 version 0.24

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Karl Broman

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Dec 18, 2020, 11:57:44 AM12/18/20
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Just posted a new version of R/qtl2 to CRAN.
The windows and Mac binaries should show up in a few days.
Use update.packages() to update your R packages, or install.packages("qtl2") to re-install R/qtl.

The biggest changes are below. There were also a number of bug fixes. For the full list of changes see https://github.com/rqtl/qtl2/blob/master/NEWS.md

karl

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Major changes
  • Revised treatment of X chromosome in "general AIL" cross type, to be the same as the autosomes but with 2/3 as many generations for recombination. This should provide a better approximation.
Minor changes
  • Revised reduce_markers() so that it can handle the case of many markers, by working with them in smaller batches.

  • fit1() now returns both fitted values and residuals.

  • fit1() can be run with genotype probabilities omitted, in which case an intercept column of 1's is used (Issue #151).

  • Updated mouse gene database with 2020-09-07 data from MGI.

  • Implemented Issue #184, to make calc_het() multi-core.

  • Made the vdiffr package optional: only test the plots locally, and only if vdiffr is installed.

  • calc_sdp() can now take a plain vector (Issue #142).

  • Added a lodcolumn argument to maxlod() (Issue #137).

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