[Genabel-commits] r971 - pkg/ProbABEL/doc

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

Author: lckarssen
Date: 2012-10-04 01:03:05 +0200 (Thu, 04 Oct 2012)
New Revision: 971

Modified:
   pkg/ProbABEL/doc/CHANGES.LOG
   pkg/ProbABEL/doc/ProbABEL_manual.tex
Log:
ProbABEL: Fixed bug #2147 The value of the Rsq column in the info file should be > 0, unlike what was mentioned in the documentation. So I updated the documentation. 



Modified: pkg/ProbABEL/doc/CHANGES.LOG
===================================================================
--- pkg/ProbABEL/doc/CHANGES.LOG	2012-10-03 22:40:55 UTC (rev 970)
+++ pkg/ProbABEL/doc/CHANGES.LOG	2012-10-03 23:03:05 UTC (rev 971)
@@ -1,14 +1,17 @@
 *****
-* Fix bug #1186: When .map file is missing (but --map option was
-  given), the wrong error message was displayed. Thanks to Nicola
-  Pirastu for reporting this bug.
-
-* Fix bug #2295: the inverse variance-covariance matrix (used with the
+* Fixed bug #2295: the inverse variance-covariance matrix (used with the
   --mmscore option) was incorrectly subsetted when NAs are present for
   one or more SNP dosages. As a result the invvarmatrix that was
   actually used in the regression contained rows and columns of
   zeroes. Thanks to Maarten Kooyman for reporting this bug.
 
+* Fixed bug #1186: When .map file is missing (but --map option was
+  given), the wrong error message was displayed. Thanks to Nicola
+  Pirastu for reporting this bug.
+
+* Fixed bug #2147: The value of the Rsq column in the info file should
+  be > 0, unlike what was mentioned in the documentation.
+
 * Update of the probabel.pl script and probabel_config.cfg.
   The .cfg file now accepts the chr separator in multiple locations in the path
   (thanks to Marijn Verkerk).

Modified: pkg/ProbABEL/doc/ProbABEL_manual.tex
===================================================================
--- pkg/ProbABEL/doc/ProbABEL_manual.tex	2012-10-03 22:40:55 UTC (rev 970)
+++ pkg/ProbABEL/doc/ProbABEL_manual.tex	2012-10-03 23:03:05 UTC (rev 971)
@@ -120,12 +120,13 @@
 metrics (``Quality'', the average maximum posterior probability and
 ``Rsq'', the proportion of variance decrease after imputations).
 
-Actually,
-for \PA{}, it does not matter what is written in this file --
-this information is just brought forward to the output. However,
-\textbf{it is critical} that the number of columns is seven 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).
+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 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}.
 
 The example of SNP information file content follows here (also
 to be found in \texttt{ProbABEL/examples/test.mlinfo})