A whole bunch of changes, including revised CC colors #197
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- Said that it gives the same thing for autosome and X chromosome, but that was fixed on [2020-09-15](rqtl@8d4c973f)
- not sure this is worth it, but it solves the NaN problem from step() for general AIL (that is, solves Issue rqtl#196)
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Major changes
The default colors for the Collaborative Cross (CC) have been changed to a color-blind friendly palette. The original CC colors remain as
CCorigcolors; the previous default is nowCCaltcolors. The new colors are derived from the palette in Wong 2011 Nature Methods.plot_coefCC()was revised to includecol=CCcolorsas an argument. The default is the new color-blind friendly CC colors, but one can now more easily usecol=CCaltcolorsorcol=CCorigcolorsto get a different choice.Minor changes
calc_het()give an error if the input are for allele dosages.Bug fixes
Fixed Issue Bug in scan1snps() if snpinfo is incomplete #195: in
create_snpinfo(), drop markers that are non-informative.Fixed Issue step() returning NaN for "genail8" #196, that
step()returns-Infrather thanNaNfor general AIL. This had to do with the handling of-Infinaddlog().In
fit1()andscan1coef(), wasn't grabbing the...arguments. properly.