[Genabel-commits] r767 - pkg/ProbABEL/doc
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Aug 24 15:37:03 CEST 2011
Author: yurii
Date: 2011-08-24 15:37:03 +0200 (Wed, 24 Aug 2011)
New Revision: 767
Added:
pkg/ProbABEL/doc/short_height_base_add.out.txt.save
pkg/ProbABEL/doc/short_test.mldose
pkg/ProbABEL/doc/test.map
pkg/ProbABEL/doc/test.mlinfo
Modified:
pkg/ProbABEL/doc/Makefile.am
pkg/ProbABEL/doc/ProbABEL_manual.tex
Log:
fixing documentation (many \verbatiminput entries were defunct)
Modified: pkg/ProbABEL/doc/Makefile.am
===================================================================
--- pkg/ProbABEL/doc/Makefile.am 2011-08-24 09:58:38 UTC (rev 766)
+++ pkg/ProbABEL/doc/Makefile.am 2011-08-24 13:37:03 UTC (rev 767)
@@ -1,8 +1,10 @@
## Process this file with automake to produce Makefile.in
-dist_doc_DATA = ProbABEL_manual.tex QuickStart.txt \
- short_coxph_data.txt short_height.out.csv \
- short_height.txt short_logist_data.txt test_regression.R \
+dist_doc_DATA = ProbABEL_manual.tex QuickStart.txt \
+ short_coxph_data.txt short_height_base_add.out.txt.save \
+ short_height.txt short_logist_data.txt short_test.mldose \
+ test.map test.mlinfo \
+ test_regression.R \
COPYING LICENSE INSTALL CHANGES.LOG TODO
Modified: pkg/ProbABEL/doc/ProbABEL_manual.tex
===================================================================
--- pkg/ProbABEL/doc/ProbABEL_manual.tex 2011-08-24 09:58:38 UTC (rev 766)
+++ pkg/ProbABEL/doc/ProbABEL_manual.tex 2011-08-24 13:37:03 UTC (rev 767)
@@ -124,9 +124,9 @@
corresponding DOSE file (plus one for the header line).
The example of SNP information file content follows here (also
-to be found in \texttt{ProbABEL/example/test.mlinfo})
+to be found in \texttt{ProbABEL/examples/test.mlinfo})
-\verbatiminput{../example/test.mlinfo}
+\verbatiminput{test.mlinfo}
Note that header line is present in the file. The file describes
five SNPs.
@@ -146,10 +146,12 @@
An example of the few first lines of an MLDOSE file for
five SNPs described in SNP information file follows here (also
-to be found in the file \texttt{../example/test.mldose})
+to be found in the file \texttt{ProbABEL/examples/test.mldose})
\verbatiminput{short_test.mldose}
+%\immediate\write18{head -n 10 INSTALL > tmp.txt}
+
\textbf{The order of SNPs in the SNP information file and DOSE-file
must be the same}. This should be the case if you just used MACH outputs.
@@ -190,7 +192,7 @@
covariates to be included into analysis.
An example few lines of phenotypic information file designed for
linear regression analysis follow here (also
-to be found in \texttt{../example/height.txt})
+to be found in \texttt{ProbABEL/examples/height.txt})
\verbatiminput{short_height.txt}
@@ -204,7 +206,7 @@
For logistic regression, it is assumed that in the second column cases are
coded as ``1'' and controls as ``0''. An couple of example lines of a phenotypic
information file designed for logistic regression analysis follow here (also
-to be found in \texttt{../example/logist\_data.txt})
+to be found in \texttt{ProbABEL/examples/logist\_data.txt})
\verbatiminput{short_logist_data.txt}
@@ -220,7 +222,7 @@
covariates to be included into the analysis. An example few lines of
a phenotypic information file designed for the Cox proportional hazards model
analysis follow here (also to be found in
-\texttt{../example/coxph\_data.txt})
+\texttt{ProbABEL/examples/coxph\_data.txt})
\verbatiminput{short_coxph_data.txt}
@@ -236,9 +238,10 @@
If you would like map information (e.g.~base pair position) to
be included in your outputs, you can supply a map file. These follow
HapMap "legend" file format. For example, for the five SNPs we considered
-the map-file may look like
+the map-file may look like (example can be found in
+\texttt{ProbABEL/examples/test.map})
-\verbatiminput{../example/test.map}
+\verbatiminput{test.map}
The order of the SNPs in the map file should follow that in the SNP information
file. Only information from the second column -- the SNP location -- is
@@ -303,10 +306,10 @@
\texttt{--info} (or \texttt{-i}),
specifying the SNP information file described in sub-section \ref{ssec:infoin}.
-If you change to the \texttt{ProbABEL/example} directory you can run
+If you change to the \texttt{ProbABEL/examples} directory you can run
an analysis of height by running
\begin{verbatim}
-user at server:~/ProbABEL/example/$ ../bin/palinear -p height.txt
+user at server:~/ProbABEL/examples/$ ../bin/palinear -p height.txt
-d test.mldose -i test.mlinfo
\end{verbatim}
Output from the analysis will be directed to the
@@ -314,13 +317,13 @@
The analysis of a binary trait (e.g.~chd) can be run with
\begin{verbatim}
-user at server:~/ProbABEL/example/$ ../bin/palogist -p logist_data.txt
+user at server:~/ProbABEL/examples/$ ../bin/palogist -p logist_data.txt
-d test.mldose -i test.mlinfo
\end{verbatim}
To run a Cox proportional hazards model, try
\begin{verbatim}
-user at server:~/ProbABEL/example/$ ../bin/pacoxph -p coxph_data.txt
+user at server:~/ProbABEL/examples/$ ../bin/pacoxph -p coxph_data.txt
-d test.mldose -i test.mlinfo
\end{verbatim}
@@ -332,7 +335,7 @@
with the \texttt{-d} option and also specify that there are two
genetic predictors per SNP, e.g.~you can run linear model with
\begin{verbatim}
-user at server:~/ProbABEL/example/$ ../bin/palinear -p height.txt
+user at server:~/ProbABEL/examples/$ ../bin/palinear -p height.txt
-d test.mlprob -i test.mlinfo
--ngpreds=2
\end{verbatim}
@@ -365,7 +368,7 @@
covariates.
An example of how a polygenic object estimated by \GA{} can be used
-with ProbABEL is provided in \texttt{../example/mmscore.R}
+with ProbABEL is provided in \texttt{ProbABEL/examples/mmscore.R}
Though technically \texttt{--mmscore} allows for inclusion of multiple
covariates, these should be kept to minimum as this is a score test. We
@@ -405,11 +408,11 @@
described in the previous section. After the analysis has run, in
the output file you will find something like
\begin{small}
-\verbatiminput{short_height.out.csv}
+\verbatiminput{short_height_base_add.out.txt.save}
\end{small}
Here, only the first three lines of output have been shown. Note that lines
-starting with \texttt{...} are actually the ones continuing the
+starting with \texttt{+>} are actually the ones continuing the
previous line -- they have just been wrapped so we can see
these long lines.
@@ -422,22 +425,22 @@
In contrast, starting with the next column, named \texttt{n},
the output concerns the data analysed. Column 8 (\texttt{n}) tells the
-number of subjects for whom complete phenotypic information was available.
-At this point, unless you have complete measurements on all
+number of subjects for whom complete phenotypic information was
+available. At this point, unless you have complete measurements on all
subjects, you should feel alarmed if the number here is exactly the
-number of people in the file -- this probably indicates you did not code
+number of people in the file -- this may indicate you did not code
missing values according to \PA{} format ('NA', 'NaN', or 'N').
The next column, nine (``Mean\_predictor\_allele''), gives the estimated
-frequency of the predictor allele in subjects with complete phenotypic data.
+frequency of the predictor allele (\texttt{A1}) in subjects with complete
+phenotypic data.
If the \texttt{--chrom} option was used, in the next column you will
find the value specified by this option. If \texttt{--map} option was
used, in the subsequent column you will find map location taken from
the map-file. The subsequent columns provide coefficients of
-regression of the phenotype onto genotype corresponding standard
-errors, and log-likelihood % $\chi^2$
-of the model at the point of MLEs.
+regression of the phenotype onto genotype, corresponding standard
+errors, and Wald $\chi^2$ test value.
\section{Preparing input files}
Added: pkg/ProbABEL/doc/short_height_base_add.out.txt.save
===================================================================
--- pkg/ProbABEL/doc/short_height_base_add.out.txt.save (rev 0)
+++ pkg/ProbABEL/doc/short_height_base_add.out.txt.save 2011-08-24 13:37:03 UTC (rev 767)
@@ -0,0 +1,6 @@
+name A1 A2 Freq1 MAF Quality Rsq n Mean_predictor_allele chrom
++> position beta_SNP_add sebeta_SNP_add chi2_SNP
+rs7247199 G A 0.5847 0.415 0.9299 0.8666 182 0.564439 19
++> 204938 -0.218693 0.734966 0.0905063
+rs8102643 C T 0.5847 0.415 0.9308 0.8685 182 0.564412 19
++> 207859 -0.218352 0.734214 0.0904094
Added: pkg/ProbABEL/doc/short_test.mldose
===================================================================
--- pkg/ProbABEL/doc/short_test.mldose (rev 0)
+++ pkg/ProbABEL/doc/short_test.mldose 2011-08-24 13:37:03 UTC (rev 767)
@@ -0,0 +1,11 @@
+1->id636728 MLDOSE 0.974 0.974 0.968 0.971 2
+2->id890314 MLDOSE 0.947 0.947 0.113 0.944 1.094
+3->id102874 MLDOSE 1.005 1.004 NaN 1.002 2
+4->id200949 MLDOSE 1.968 1.969 1.973 1.977 2
+5->id336491 MLDOSE 1.007 1.006 1.001 1.004 2
+6->id988766 MLDOSE 1.006 1.006 1 1.003 2
+7->id21999 MLDOSE 1.968 1.969 1.973 1.977 2
+8->id433893 MLDOSE 1.006 1.006 1.001 1.004 2
+9->id688932 MLDOSE 1.006 1.006 1.001 1.004 2
+10->id394203 MLDOSE 1.967 1.968 1.972 1.976 1.999
+11->id995678 MLDOSE 1.014 1.014 1.006 1.009 2
Added: pkg/ProbABEL/doc/test.map
===================================================================
--- pkg/ProbABEL/doc/test.map (rev 0)
+++ pkg/ProbABEL/doc/test.map 2011-08-24 13:37:03 UTC (rev 767)
@@ -0,0 +1,6 @@
+rs position 0 1
+rs7247199 204938 A G
+rs8102643 207859 C T
+rs8102615 211970 A T
+rs8105536 212033 A G
+rs2312724 217034 C T
Added: pkg/ProbABEL/doc/test.mlinfo
===================================================================
--- pkg/ProbABEL/doc/test.mlinfo (rev 0)
+++ pkg/ProbABEL/doc/test.mlinfo 2011-08-24 13:37:03 UTC (rev 767)
@@ -0,0 +1,6 @@
+SNP Al1 Al2 Freq1 MAF Quality Rsq
+rs7247199 G A 0.5847 0.4150 0.9299 0.8666
+rs8102643 C T 0.5847 0.4150 0.9308 0.8685
+rs8102615 T A 0.5006 0.4702 0.9375 0.8932
+rs8105536 G A 0.5783 0.4213 0.9353 0.8832
+rs2312724 T C 0.9122 0.0877 0.9841 0.9232
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