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rqtl / qtl2

QTL analysis software for high-dimensional data and complex cross designs
https://kbroman.org/qtl2
GNU General Public License v3.0
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step() returning NaN for "genail8" #196

Closed kbroman closed 3 years ago

kbroman commented 3 years ago

step(), which gives the log transition probability, should give 0.0 or -Inf when r=0, but for cross type "genail8" it gives NaN for some genotype pairs.

To or from a homozygous genotype looks okay, but between heterozygous genotypes we're getting the NaN results.

kbroman commented 3 years ago

Should look at step_genchr()

kbroman commented 3 years ago

It was coming from the combination of values in GENAIL::step, and is due to addlog(-Inf, -Inf) giving NaN. Not sure the fix in addlog() was worth it.