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[#2147] ProbABEL output has 'nan' when values in info file are zero
Lennart Karssen (
Lennart Karssen (lckarssen)
ProbABEL output has 'nan' when values in info file are zero
In the ProbABEL manual we write that the actual values in the info file are not important and that they are simply copied to the output. It turns out that if the values are 0 the beta and se_beta columns (and loglik as well) are set to 'nan'.
This is described in more detail on the forum:
Thanks to forum member vforgetta for pointing this out!
Date: 2012-10-03 23:03
Fixed the documentation in SVN r.971.
Date: 2012-07-13 15:34
Actually, the problem is in the Rsq column. If that is 0 (or 0.0) the output of beta etc. is set to 'nan'.
In main.cpp, line 751 a test is done for Rsq:
if (fabs(mli.Rsq[csnp])<1.e-16) poly=0;
this poly variable is then used to decide whether to print 'nan' for beta etc. (if() in line 771 and else in line 836). The poly variable is true if the allele is not rare.
Accepted As Bug