[Genabel-commits] r845 - pkg/ProbABEL/doc

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

Author: lckarssen
Date: 2012-02-22 02:14:22 +0100 (Wed, 22 Feb 2012)
New Revision: 845

Added:
   pkg/ProbABEL/doc/palinear.1
Modified:
   pkg/ProbABEL/doc/Makefile.am
Log:
Added a man page for palinear (that gets installed automatically by make install). man pages for palogist and pacoxph will follow soon.

Modified: pkg/ProbABEL/doc/Makefile.am
===================================================================
--- pkg/ProbABEL/doc/Makefile.am	2012-02-22 00:22:14 UTC (rev 844)
+++ pkg/ProbABEL/doc/Makefile.am	2012-02-22 01:14:22 UTC (rev 845)
@@ -6,6 +6,8 @@
  test.mlinfo test_regression.R COPYING LICENSE INSTALL CHANGES.LOG	\
  TODO
 
+man_MANS = palinear.1
+EXTRA_DIST = $(man_MANS)
 
 if HAVE_PDFLATEX
 MANNAME = ProbABEL_manual

Added: pkg/ProbABEL/doc/palinear.1
===================================================================
--- pkg/ProbABEL/doc/palinear.1	                        (rev 0)
+++ pkg/ProbABEL/doc/palinear.1	2012-02-22 01:14:22 UTC (rev 845)
@@ -0,0 +1,82 @@
+.TH palinear 1 "22 February 2012"
+.SH NAME
+palinear \- Perform Genome-Wide Association Analysis using a linear model
+.SH SYNOPSIS
+.B palinear
+.RI "[ " "command-line options" " ]"
+.SH DESCRIPTION
+.I palinear
+runs a linear regression in an efficient way.
+.SH Options
+.SS Required command line options
+.TP
+.BI "\-\^\-pheno" " FILE"
+Read phenotype data from
+.I FILE
+.TP
+.BI "\-\^\-info" " FILE"
+Read SNP information from
+.I FILE
+(e.g. MLINFO file)
+.TP
+.BI "\-\^\-dose" " FILE"
+SNP predictor (e.g. MLDOSE/MLPROB) file name
+.SS Optional command line options
+.TP
+.BI "\-\^\-map" " FILE"
+Map file name, containing base pair positions for each SNP.
+.TP
+.BI "\-\^\-nids" " NUMBER"
+Number of people to analyse
+.TP
+.BI "\-\^\-chrom"  " FILE"
+Chromosome (to be passed to output)
+.TP
+.BI "\-\^\-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)
+.TP
+.BI "\-\^\-ntraits" " NUMBER"
+How many traits are analysed (default is 1)
+.TP
+.BI "\-\^\-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)
+.TP
+.B \-\^\-score
+Use the score test
+.TP
+.B \-\^\-no-head
+Do not report header line in the output
+.TP
+.B \-\^\-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)
+.TP
+.B \-\^\-interaction_only
+Like
+.B \-\^\-interaction
+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 palinear) or inverse correlation (for palogist) as input parameter
+.TP
+.B \-\^\-robust
+Report robust (aka sandwich, aka Hubert-White) standard errors
+.TP
+.B \-\^\-help
+Print help
+
+.SH "SEE ALSO"
+palogist(1), pacoxph(1)
+.SH BUGS
+.SH AUTHORS
+Lennart C. Karssen