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[#2147] ProbABEL output has 'nan' when values in info file are zero

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Date:
2012-07-13 15:01
Priority:
3
State:
Closed
Submitted by:
Lennart Karssen (lckarssen)
Assigned to:
Lennart Karssen (lckarssen)
Resolution:
Fixed
Operating System:
All
Severity:
minor
Hardware:
All
Version:
PA v0.2.0
Component:
ProbABEL
URL:
http://forum.genabel.org/viewtopic.php?f=10&t=663
 
Summary:
ProbABEL output has 'nan' when values in info file are zero

Detailed description
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: http://forum.genabel.org/viewtopic.php?f=10&t=663

Thanks to forum member vforgetta for pointing this out!

Followup

Message
Date: 2012-10-03 23:03
Sender: Lennart Karssen

Fixed the documentation in SVN r.971.
Date: 2012-07-13 15:34
Sender: Lennart Karssen

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.

Attached Files:

Changes:

Field Old Value Date By
ResolutionAccepted As Bug2012-10-03 23:03lckarssen
close_dateNone2012-10-03 23:03lckarssen
status_idOpen2012-10-03 23:03lckarssen
assigned_tonone2012-07-13 15:34lckarssen
Thanks to:
Vienna University of Economics and Business University of Wisconsin - Madison Powered By FusionForge