[Genabel-commits] r1975 - branches/ProbABEL-v0.4.4-hotfix/ProbABEL/doc

[noreply at r-forge.r-project.org]

Author: lckarssen
Date: 2015-05-14 17:58:46 +0200 (Thu, 14 May 2015)
New Revision: 1975

Modified:
   branches/ProbABEL-v0.4.4-hotfix/ProbABEL/doc/ChangeLog
   branches/ProbABEL-v0.4.4-hotfix/ProbABEL/doc/ProbABEL_manual.tex
Log:
Fixed incorrect documentation of minimum value for the Rsq column in ProbABEL's info file (should be > 1e-16 instead of > 0).

Thanks to forum user quentin300 for reporting this: http://forum.genabel.org/viewtopic.php?f=10&t=941


Modified: branches/ProbABEL-v0.4.4-hotfix/ProbABEL/doc/ChangeLog
===================================================================
--- branches/ProbABEL-v0.4.4-hotfix/ProbABEL/doc/ChangeLog	2015-05-11 19:37:36 UTC (rev 1974)
+++ branches/ProbABEL-v0.4.4-hotfix/ProbABEL/doc/ChangeLog	2015-05-14 15:58:46 UTC (rev 1975)
@@ -1,6 +1,7 @@
 ***** v.0.4.5 (2015)
 * Fixed bug #6054: "Not all ProbABEL's short command line options are
   correctly parsed."
+* Minor fix to the manual: the Rsq values in the info file should be > 1e-16 otherwise the output will be set to 'nan'.
 
 
 ***** v.0.4.4 (2014.11.07)

Modified: branches/ProbABEL-v0.4.4-hotfix/ProbABEL/doc/ProbABEL_manual.tex
===================================================================
--- branches/ProbABEL-v0.4.4-hotfix/ProbABEL/doc/ProbABEL_manual.tex	2015-05-11 19:37:36 UTC (rev 1974)
+++ branches/ProbABEL-v0.4.4-hotfix/ProbABEL/doc/ProbABEL_manual.tex	2015-05-14 15:58:46 UTC (rev 1975)
@@ -306,12 +306,13 @@
 Actually, for \PA{}, it (almost) does not matter what is written in
 this file -- this information is simply copied to the output. However,
 \textbf{it is critical} that the number of columns is
-seven\footnote{This means that for \texttt{minimac} output files the number of
-  columns needs to be reduced. This can be done using e.g.~GAWK or
-  \texttt{cut}.} and the number of lines in the file is equal to the
-number of SNPs in the corresponding DOSE file (plus one for the header
-line). Also make sure that the ``Rsq'' column contains values $>0$,
-otherwise you will end up with $\beta$'s set to \texttt{nan}.
+seven\footnote{This means that for \texttt{minimac} output files the
+  number of columns needs to be reduced. This can be done using
+  e.g.~GAWK or \texttt{cut}.} and the number of lines in the file is
+equal to the number of SNPs in the corresponding DOSE file (plus one
+for the header line). Also make sure that the ``Rsq'' column contains
+values $>1 \cdot 10^{-16}$, otherwise you will end up with $\beta$'s
+set to \texttt{nan}.
 
 The example of SNP information file content follows here (also
 to be found in \texttt{ProbABEL/examples/test.mlinfo})