[Genabel-commits] r1246 - pkg/ProbABEL/doc
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Jun 13 20:35:45 CEST 2013
Author: lckarssen
Date: 2013-06-13 20:35:45 +0200 (Thu, 13 Jun 2013)
New Revision: 1246
Modified:
pkg/ProbABEL/doc/ProbABEL_manual.tex
pkg/ProbABEL/doc/pacoxph.1
pkg/ProbABEL/doc/palinear.1
pkg/ProbABEL/doc/palogist.1
Log:
- Updated man pages; included the short option forms
- Updated the manual for the upcoming release, removed footnotes about pacoxph being buggy and updated screen output to the latest from.
Modified: pkg/ProbABEL/doc/ProbABEL_manual.tex
===================================================================
--- pkg/ProbABEL/doc/ProbABEL_manual.tex 2013-06-13 05:52:45 UTC (rev 1245)
+++ pkg/ProbABEL/doc/ProbABEL_manual.tex 2013-06-13 18:35:45 UTC (rev 1246)
@@ -1,6 +1,6 @@
\documentclass[12pt,a4paper]{article}
-\title{Manual for ProbABEL v0.3.0}
+\title{Manual for ProbABEL v0.4.0}
\author{
Maksim Struchalin$^{1}$, Lennart Karssen$^{1}$, Yurii Aulchenko$^{2}$ \\
\\
@@ -277,14 +277,16 @@
There are in total 11 command line options you can specify to the
\PA{} analysis functions \texttt{palinear} or \texttt{palogist}. If
-you run either program without any argument or with the
-\texttt{--help} option, you will get a short explanation to command
-line options:
+you run either program with the \texttt{--help} option, you will get a
+short explanation to the command line options:
\begin{verbatim}
-user at server:~$ palogist
-ProbABEL v. 0.2.0 (C) Yurii Aulchenko, Lennart C. Karssen, Maksim Struchalin, EMCR
+user at server:~$ palogist --help
+probabel v. 0.4.0
+(C) Yurii Aulchenko, Lennart C. Karssen, Maksim Struchalin, EMCR
-Usage: /tmp/PAInst/bin/palogist options
+Using EIGEN version 3.1.2 for matrix operations
+
+Usage: src/palogist options
Options:
--pheno : phenotype file name
--info : information (e.g. MLINFO) file name
@@ -294,7 +296,7 @@
--chrom : [optional] chromosome (to be passed to output)
--out : [optional] output file name (default is regression.out.txt)
--skipd : [optional] how many columns to skip in the predictor
- (dose/prob) file (default 2)
+ (dose/prob) file (default 2)
--ntraits : [optional] how many traits are analysed (default 1)
--ngpreds : [optional] how many predictor columns per marker
(default 1 = MLDOSE; else use 2 for MLPROB)
@@ -308,9 +310,13 @@
--robust : report robust (aka sandwich, aka Hubert-White) standard errors
--help : print help
\end{verbatim}
-%% --interaction_only: like previos but without covariate acting in
-%% interaction with SNP
-%% (default is no ineraction, 0)
+More information on the options can also be found in the manual page
+of each of the programs. For example, to access the manual page for
+\texttt{palinear} on a Linux system run\footnote{Use the \texttt{q}
+ key to quit the man page viewer.}:
+\begin{verbatim}
+user at server$ man palinear
+\end{verbatim}
\subsection{Basic analysis options}
@@ -828,7 +834,7 @@
\end{quote}
A proper reference may look like
\begin{quote}
-For the analysis of imputed data, we used the \PA{} v.0.3.0
+For the analysis of imputed data, we used the \PA{} v.0.4.0
from the \texttt{GenABEL} suite of programs (Aulchenko \emph{et al.}, 2010).
\end{quote}
Modified: pkg/ProbABEL/doc/pacoxph.1
===================================================================
--- pkg/ProbABEL/doc/pacoxph.1 2013-06-13 05:52:45 UTC (rev 1245)
+++ pkg/ProbABEL/doc/pacoxph.1 2013-06-13 18:35:45 UTC (rev 1246)
@@ -17,67 +17,69 @@
.BI "\-i, \-\^\-info" " FILE"
Read SNP information from
.I FILE
-(e.g. MLINFO file)
+(e.g. MLINFO file).
.TP
.BI "\-d, \-\^\-dose" " FILE"
-SNP predictor (e.g. MLDOSE/MLPROB) file name
+SNP predictor (e.g. MLDOSE/MLPROB) file name.
.SS Optional command line options
.TP
-.BI "\-\^\-map" " FILE"
+.BI "\-m, \-\^\-map" " FILE"
Map file name, containing base pair positions for each SNP.
.TP
-.BI "\-\^\-nids" " NUMBER"
-Number of people to analyse
+.BI "\-n, \-\^\-nids" " NUMBER"
+Number of people to analyse.
.TP
-.BI "\-\^\-chrom" " FILE"
-Chromosome (to be passed to output)
+.BI "\-c, \-\^\-chrom" " FILE"
+Chromosome (to be passed to output).
.TP
-.BI "\-\^\-out" " FILE"
+.BI "\-o, \-\^\-out" " FILE"
Output file name (default is
.B regression.out.txt
-)
+).
.TP
-.BI "\-\^\-skipd" " NUMBER"
-How many columns to skip in predictor (dose/prob) file (default is 2)
+.BI "\-s, \-\^\-skipd" " NUMBER"
+How many columns to skip in predictor (dose/prob) file (default is 2).
.TP
-.BI "\-\^\-ntraits" " NUMBER"
-How many traits are analysed (default is 2)
+.BI "\-t, \-\^\-ntraits" " NUMBER"
+How many traits are analysed (default is 2).
.TP
-.BI "\-\^\-ngpreds" " NUMBER"
-How many predictor columns per marker (default 1 = MLDOSE; else use 2 for MLPROB)
+.BI "\-g, \-\^\-ngpreds" " NUMBER"
+How many predictor columns per marker (default 1 = MLDOSE; else use 2 for MLPROB).
.TP
-.B "\-\^\-separat" " FILE"
-Character to separate fields (default is space)
+.B "\-a, \-\^\-separat" " FILE"
+Character to separate fields (default is space).
.TP
-.B \-\^\-score
-Use the score test
+.B \-r, \-\^\-score
+Use the score test.
.TP
-.B \-\^\-no-head
-Do not report header line in the output
+.B \-e, \-\^\-no-head
+Do not report header line in the output.
.TP
-.B \-\^\-allcov
-Report estimates for all covariates (large outputs!)
+.B \-l \-\^\-allcov
+Report estimates for all covariates (large outputs!).
.TP
-.B \-\^\-interaction
-Which covariate to use for interaction with SNP analysis (default is no interaction, 0)
+.B \-b, \-\^\-interaction
+Which covariate to use for interaction with SNP analysis (default is no interaction, 0).
.TP
-.B \-\^\-interaction_only
+.B \-k, \-\^\-interaction_only
Like
.B \-\^\-interaction
-but without covariate acting in interaction with SNP (default is no interaction, 0)
+but without covariate acting in interaction with SNP (default is no interaction, 0).
.TP
.BI "\-\^\-mmscore" " FILE"
-Score test in samples of related individuals. File with inverse of variance-covariance matrix (for pacoxph) or inverse correlation (for palogist) as input parameter
+Score test in samples of related individuals. The FILE argument is the name of a file with the inverse of the variance-covariance matrix.
.TP
-.B \-\^\-robust
-Report robust (a.k.a. sandwich, a.k.a. Hubert-White) standard errors
+.B \-u, \-\^\-robust
+Report robust (a.k.a. sandwich, a.k.a. Hubert-White) standard errors.
.TP
.B \-\^\-help
-Print help
+Print help.
.SH "SEE ALSO"
palinear(1), palogist(1)
.SH BUGS
-None known at the moment. The bugtracker is located at https://r-forge.r-project.org/tracker/?group_id=505
+The bugtracker is located at
+.br
+https://r-forge.r-project.org/tracker/?group_id=505
.SH AUTHORS
Lennart C. Karssen
Modified: pkg/ProbABEL/doc/palinear.1
===================================================================
--- pkg/ProbABEL/doc/palinear.1 2013-06-13 05:52:45 UTC (rev 1245)
+++ pkg/ProbABEL/doc/palinear.1 2013-06-13 18:35:45 UTC (rev 1246)
@@ -23,60 +23,63 @@
SNP predictor (e.g. MLDOSE/MLPROB) file name.
.SS Optional command line options
.TP
-.BI "\-\^\-map" " FILE"
+.BI "\-m, \-\^\-map" " FILE"
Map file name, containing base pair positions for each SNP.
.TP
-.BI "\-\^\-nids" " NUMBER"
+.BI "\-n, \-\^\-nids" " NUMBER"
Number of people to analyse.
.TP
-.BI "\-\^\-chrom" " FILE"
+.BI "\-c, \-\^\-chrom" " FILE"
Chromosome (to be passed to output).
.TP
-.BI "\-\^\-out" " FILE"
+.BI "\-o, \-\^\-out" " FILE"
Output file name (default is
.B regression.out.txt
).
.TP
-.BI "\-\^\-skipd" " NUMBER"
+.BI "\-s, \-\^\-skipd" " NUMBER"
How many columns to skip in predictor (dose/prob) file (default is 2).
.TP
-.BI "\-\^\-ntraits" " NUMBER"
+.BI "\-t, \-\^\-ntraits" " NUMBER"
How many traits are analysed (default is 1).
.TP
-.BI "\-\^\-ngpreds" " NUMBER"
+.BI "\-g, \-\^\-ngpreds" " NUMBER"
How many predictor columns per marker (default 1 = MLDOSE; else use 2 for MLPROB).
.TP
-.B "\-\^\-separat" " FILE"
+.B "\-a, \-\^\-separat" " FILE"
Character to separate fields (default is space).
.TP
-.B \-\^\-score
+.B \-r, \-\^\-score
Use the score test.
.TP
-.B \-\^\-no-head
+.B \-e, \-\^\-no-head
Do not report header line in the output.
.TP
-.B \-\^\-allcov
+.B \-l \-\^\-allcov
Report estimates for all covariates (large outputs!).
.TP
-.B \-\^\-interaction
+.B \-b, \-\^\-interaction
Which covariate to use for interaction with SNP analysis (default is no interaction, 0).
.TP
-.B \-\^\-interaction_only
+.B \-k, \-\^\-interaction_only
Like
.B \-\^\-interaction
but without covariate acting in interaction with SNP (default is no interaction, 0).
.TP
-.BI "\-\^\-mmscore" " FILE"
+.BI "\-v, \-\^\-mmscore" " FILE"
Score test in samples of related individuals. The FILE argument is the name of a file with the inverse of the variance-covariance matrix.
.TP
-.B \-\^\-robust
+.B \-u, \-\^\-robust
Report robust (a.k.a. sandwich, a.k.a. Hubert-White) standard errors.
.TP
.B \-\^\-help
-Print help
+Print help.
.SH "SEE ALSO"
palogist(1), pacoxph(1)
.SH BUGS
+The bugtracker is located at
+.br
+https://r-forge.r-project.org/tracker/?group_id=505
.SH AUTHORS
Lennart C. Karssen
Modified: pkg/ProbABEL/doc/palogist.1
===================================================================
--- pkg/ProbABEL/doc/palogist.1 2013-06-13 05:52:45 UTC (rev 1245)
+++ pkg/ProbABEL/doc/palogist.1 2013-06-13 18:35:45 UTC (rev 1246)
@@ -23,50 +23,50 @@
SNP predictor (e.g. MLDOSE/MLPROB) file name.
.SS Optional command line options
.TP
-.BI "\-\^\-map" " FILE"
+.BI "\-m, \-\^\-map" " FILE"
Map file name, containing base pair positions for each SNP.
.TP
-.BI "\-\^\-nids" " NUMBER"
+.BI "\-n, \-\^\-nids" " NUMBER"
Number of people to analyse.
.TP
-.BI "\-\^\-chrom" " FILE"
+.BI "\-c, \-\^\-chrom" " FILE"
Chromosome (to be passed to output).
.TP
-.BI "\-\^\-out" " FILE"
+.BI "\-o, \-\^\-out" " FILE"
Output file name (default is
.B regression.out.txt
).
.TP
-.BI "\-\^\-skipd" " NUMBER"
+.BI "\-s, \-\^\-skipd" " NUMBER"
How many columns to skip in predictor (dose/prob) file (default is 2).
.TP
-.BI "\-\^\-ntraits" " NUMBER"
+.BI "\-t, \-\^\-ntraits" " NUMBER"
How many traits are analysed (default is 1).
.TP
-.BI "\-\^\-ngpreds" " NUMBER"
+.BI "\-g, \-\^\-ngpreds" " NUMBER"
How many predictor columns per marker (default 1 = MLDOSE; else use 2 for MLPROB).
.TP
-.B "\-\^\-separat" " FILE"
+.B "\-a, \-\^\-separat" " FILE"
Character to separate fields (default is space).
.TP
-.B \-\^\-score
+.B \-r, \-\^\-score
Use the score test.
.TP
-.B \-\^\-no-head
+.B \-e, \-\^\-no-head
Do not report header line in the output.
.TP
-.B \-\^\-allcov
+.B \-l \-\^\-allcov
Report estimates for all covariates (large outputs!).
.TP
-.B \-\^\-interaction
+.B \-b, \-\^\-interaction
Which covariate to use for interaction with SNP analysis (default is no interaction, 0).
.TP
-.B \-\^\-interaction_only
+.B \-k, \-\^\-interaction_only
Like
.B \-\^\-interaction
but without covariate acting in interaction with SNP (default is no interaction, 0).
.TP
-.BI "\-\^\-mmscore" " FILE"
+.BI "\-v, \-\^\-mmscore" " FILE"
Score test in samples of related individuals. The FILE argument is the name of a file with the inverse correlation matrix. NOTE THAT THIS FEATURE IS STILL EXPERIMENTAL!
.TP
.B \-\^\-robust
@@ -78,5 +78,8 @@
.SH "SEE ALSO"
palinear(1), pacoxph(1)
.SH BUGS
+The bugtracker is located at
+.br
+https://r-forge.r-project.org/tracker/?group_id=505
.SH AUTHORS
Lennart C. Karssen
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