NEWS.md

In mmconvert: Mouse Map Converter

mmconvert 0.10 (2023-04-25)

• Omit X chr positions if input_type is "ave_cM" or "male_cM" (Issue #9)

mmconvert 0.8 (2023-03-29)

• Small changes for CRAN submission.

mmconvert 0.6 (2023-03-28)

• Added dataset grcm39_chrlen with lengths of GRCm39 chromosomes in basepairs.

• Revised mmconvert to give warnings if inferred positions are outside of the range of chromosomes in GRCm39. (Issue #7)

• In cross2_to_grcm39() when using "guess", only pick the GM/MM combination if it gives >20 additional markers than either GM or MM on their own.

• Replaced the coxmap object with a smoothed version (using the R/qtl2 function smooth_gmap() with alpha=0.02), with intervals with 0 recombination smoothed out to allow some recombination. The mmconvert() function uses this version of the Cox maps, and so gives interpolated positions that are similarly smoothed. Included a script smooth_coxmaps.R that does the work.

• Revised the MUGA array datasets to use this "smoothed" version of the Cox maps.

mmconvert 0.4 (2023-03-22)

• Revised Cox genetic maps, estimated using the original crimap software.

• Revised MUGAmaps, using the corrected Cox genetic maps.

• Revised cross2_to_grcm39() so that it will also consider that markers are from the combination of GigaMUGA and MegaMUGA arrays (Issue #6).

mmconvert 0.2-4 (2021-10-13)

• Added a dataset with the MUGA array annotations for markers on the autosomes or X chromosome, with mouse build GRCm39 positions and the revised Cox Map genetic map locations.

• Add function cross2_to_grcm39() for converting an R/qtl2 cross2 object to use the new GRCm39 mouse build and the revised Cox genetic map.

mmconvert 0.1-5 (2021-09-28)

• New package

mmconvert documentation built on April 25, 2023, 5:13 p.m.