mmconvert().
(Issue #10.)input_type is "ave_cM" or "male_cM"
(Issue #9)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.
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).
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.