From fc516ae334ef68d453aeece8de521ff76017b811 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Wed, 30 Sep 2020 08:54:29 +0100
Subject: Added information on disabling filters

Relates to #234
---
 doc/manual.pdf | Bin 319480 -> 272474 bytes
 doc/manual.tex |  15 ++++++++-------
 2 files changed, 8 insertions(+), 7 deletions(-)

(limited to 'doc')

diff --git a/doc/manual.pdf b/doc/manual.pdf
index 1b7dc5d..0980ea6 100644
Binary files a/doc/manual.pdf and b/doc/manual.pdf differ
diff --git a/doc/manual.tex b/doc/manual.tex
index 73acb60..1cf0400 100644
--- a/doc/manual.tex
+++ b/doc/manual.tex
@@ -733,21 +733,24 @@ The are a few SNP filters implemented in the software.
 
 \item Missingness. By default, SNPs with missingness below 5\% will
   not be included in the analysis. Use ``-miss [num]'' to change. For
-  example, ``-miss 0.1'' changes the threshold to 10\%.
+  example, ``-miss 0.1'' changes the threshold to 10\%. With
+  ``-miss 1.0'' the filter is disabled.
 
 \item Minor allele frequency. By default, SNPs with minor allele
   frequency below 1\% will not be included in the analysis. Use ``-maf
   [num]" to change. For example, ``-maf 0.05'' changes the threshold
-  to 5\%.
+  to 5\%. With ``-notsnp'' the filter is disabled.
 
 \item Correlation with any covariate. By default, SNPs with $r^2$
   correlation with any of the covariates above 0.9999 will not be
   included in the analysis. Use ``-r2 [num]'' to change. For example,
-  ``-r2 0.999999'' changes the threshold to 0.999999.
+  ``-r2 0.999999'' changes the threshold to 0.999999.  With ``-r2
+  1.0'' the filter is disabled.
 
 \item Hardy-Weinberg equilibrium. Use ``-hwe [num]'' to specify. For
   example, ``-hwe 0.001'' will filter out SNPs with Hardy-Weinberg $p$
-  values below 0.001.
+  values below 0.001.  With ``-hwe 0'' or ``--notsnp'' the filter is
+  disabled.
 
 \item User-defined SNP list. Use ``-snps [filename]'' to specify a
   list of SNPs to be included in the analysis.
@@ -1452,7 +1455,7 @@ You can use -outdir with gemma as a bash script
 \end{verbatim}
 
 makes a unique temp directory where the output is stored, here
-relative to $HOME, but you can take any path.
+relative to \$HOME, but you can take any path.
 
 
 \subsection{How do I prepare the phenotype file for BSLMM?}
@@ -1480,8 +1483,6 @@ prefix.prdt.txt file will match the total sample size. Please refer to
 the GWAS sample data set and some demo scripts included with the GEMMA
 source code for detailed examples.
 
-\end{enumerate}
-
 \clearpage
 \newpage
 
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