[Genabel-commits] r1304 - in pkg/ProbABEL: doc src

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

Author: lckarssen
Date: 2013-08-25 16:27:15 +0200 (Sun, 25 Aug 2013)
New Revision: 1304

Modified:
   pkg/ProbABEL/doc/pacoxph.1
   pkg/ProbABEL/src/command_line_settings.cpp
   pkg/ProbABEL/src/usage.cpp
Log:
Remove options from the man page and the help output that are not allowed/implemented with pacoxph.



Modified: pkg/ProbABEL/doc/pacoxph.1
===================================================================
--- pkg/ProbABEL/doc/pacoxph.1	2013-08-25 11:49:57 UTC (rev 1303)
+++ pkg/ProbABEL/doc/pacoxph.1	2013-08-25 14:27:15 UTC (rev 1304)
@@ -1,4 +1,4 @@
-.TH pacoxph 1 "23 August 2013"
+.TH pacoxph 1 "25 August 2013"
 .SH NAME
 pacoxph \- Perform Genome-Wide Association Analysis using a linear model
 .SH SYNOPSIS
@@ -66,12 +66,6 @@
 .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. The FILE argument is the name of a file with the inverse of the variance-covariance matrix.
-.TP
-.B \-u, \-\^\-robust
-Report robust (a.k.a. sandwich, a.k.a. Hubert-White) standard errors.
-.TP
 .B \-\^\-help
 Print help.
 

Modified: pkg/ProbABEL/src/command_line_settings.cpp
===================================================================
--- pkg/ProbABEL/src/command_line_settings.cpp	2013-08-25 11:49:57 UTC (rev 1303)
+++ pkg/ProbABEL/src/command_line_settings.cpp	2013-08-25 14:27:15 UTC (rev 1304)
@@ -208,9 +208,11 @@
         case 'e':
             nohead = 1;
             break;
+#if !COXPH
         case 'r':
             score = 1;
             break;
+#endif
         case 'l':
             allcov = 1;
             break;
@@ -220,12 +222,14 @@
         case 'k':
             interaction_excluded = atoi(optarg);
             break;
+#if !COXPH
         case 'v':
             inverse_filename = optarg;
             break;
         case 'u':
             robust = 1;
             break;
+#endif
 
         case '?':
             print_usage(program_name, 2);

Modified: pkg/ProbABEL/src/usage.cpp
===================================================================
--- pkg/ProbABEL/src/usage.cpp	2013-08-25 11:49:57 UTC (rev 1303)
+++ pkg/ProbABEL/src/usage.cpp	2013-08-25 14:27:15 UTC (rev 1304)
@@ -46,7 +46,9 @@
     cout << "\t --separat : [optional] character to separate fields "
          << "(default is space)"
          << endl;
+#if !COXPH
     cout << "\t --score   : use score test" << endl;
+#endif
     cout << "\t --no-head : do not report header line" << endl;
     cout << "\t --allcov  : report estimates for all covariates (large outputs!)"
          << endl;
@@ -56,6 +58,7 @@
     cout << "\t --interaction_only: like previous but without covariate acting"
          << " in interaction with SNP (default is no interaction, 0)"
          << endl;
+#if !COXPH
     cout << "\t --mmscore : score test in samples of related individuals. "
          << "File with inverse of variance-covariance matrix (for palinear)"
          << " or inverse correlation (for palogist) as input parameter"
@@ -63,6 +66,7 @@
     cout << "\t --robust  : report robust (aka sandwich, aka Hubert-White) "
          << "standard errors"
          << endl;
+#endif
     cout << "\t --help    : print help" << endl;
     exit(exit_code);
 }