[Genabel-commits] r1747 - in pkg/ProbABEL: doc src
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue May 27 13:38:12 CEST 2014
Author: lckarssen
Date: 2014-05-27 13:38:11 +0200 (Tue, 27 May 2014)
New Revision: 1747
Modified:
pkg/ProbABEL/doc/pacoxph.1
pkg/ProbABEL/doc/palinear.1
pkg/ProbABEL/doc/palogist.1
pkg/ProbABEL/src/reg1.cpp
Log:
Improved the Doxygen documentation for the apply_model() function. Also improved the man pages w.r.t. the explanation of the options for interaction analysis.
Modified: pkg/ProbABEL/doc/pacoxph.1
===================================================================
--- pkg/ProbABEL/doc/pacoxph.1 2014-05-27 09:56:07 UTC (rev 1746)
+++ pkg/ProbABEL/doc/pacoxph.1 2014-05-27 11:38:11 UTC (rev 1747)
@@ -46,7 +46,7 @@
.BI "\-g, \-\^\-ngpreds" " NUMBER"
How many predictor columns per marker (default 1 = MLDOSE; else use 2 for MLPROB).
.TP
-.B "\-a, \-\^\-separat" " FILE"
+.BI "\-a, \-\^\-separat" " FILE"
Character to separate fields (default is space).
.TP
.B \-r, \-\^\-score
@@ -58,19 +58,19 @@
.B \-l \-\^\-allcov
Report estimates for all covariates (large outputs!).
.TP
-.B \-b, \-\^\-interaction
-Which covariate to use for interaction with SNP analysis (default is no interaction, 0).
+.BI "\-b, \-\^\-interaction" " NUMBER"
+Which covariate to use for interaction with SNP analysis (default is no interaction, 0). \fINUMBER\fR indicates the column number of the covariate.
.TP
-.B \-k, \-\^\-interaction_only
+.BI "\-k, \-\^\-interaction_only" " NUMBER"
Like
.B \-\^\-interaction
-but without covariate acting in interaction with SNP (default is no interaction, 0).
+but excludes the covariate-only model term for the covariate acting in interaction with the SNP (default is no interaction, 0).
.TP
.B \-\^\-help
Print help.
.SH "SEE ALSO"
-palinear(1), palogist(1)
+probabel(1), palinear(1), palogist(1)
.SH BUGS
The bugtracker is located at
.br
Modified: pkg/ProbABEL/doc/palinear.1
===================================================================
--- pkg/ProbABEL/doc/palinear.1 2014-05-27 09:56:07 UTC (rev 1746)
+++ pkg/ProbABEL/doc/palinear.1 2014-05-27 11:38:11 UTC (rev 1747)
@@ -46,7 +46,7 @@
.BI "\-g, \-\^\-ngpreds" " NUMBER"
How many predictor columns per marker (default 1 = MLDOSE; else use 2 for MLPROB).
.TP
-.B "\-a, \-\^\-separat" " FILE"
+.BI "\-a, \-\^\-separat" " FILE"
Character to separate fields (default is space).
.TP
.B \-r, \-\^\-score
@@ -58,13 +58,13 @@
.B \-l \-\^\-allcov
Report estimates for all covariates (large outputs!).
.TP
-.B \-b, \-\^\-interaction
-Which covariate to use for interaction with SNP analysis (default is no interaction, 0).
+.BI "\-b, \-\^\-interaction" " NUMBER"
+Which covariate to use for interaction with SNP analysis (default is no interaction, 0). \fINUMBER\fR indicates the column number of the covariate.
.TP
-.B \-k, \-\^\-interaction_only
+.BI "\-k, \-\^\-interaction_only" " NUMBER"
Like
.B \-\^\-interaction
-but without covariate acting in interaction with SNP (default is no interaction, 0).
+but excludes the covariate-only model term for the covariate acting in interaction with the SNP (default is no interaction, 0).
.TP
.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.
Modified: pkg/ProbABEL/doc/palogist.1
===================================================================
--- pkg/ProbABEL/doc/palogist.1 2014-05-27 09:56:07 UTC (rev 1746)
+++ pkg/ProbABEL/doc/palogist.1 2014-05-27 11:38:11 UTC (rev 1747)
@@ -46,7 +46,7 @@
.BI "\-g, \-\^\-ngpreds" " NUMBER"
How many predictor columns per marker (default 1 = MLDOSE; else use 2 for MLPROB).
.TP
-.B "\-a, \-\^\-separat" " FILE"
+.BI "\-a, \-\^\-separat" " FILE"
Character to separate fields (default is space).
.TP
.B \-r, \-\^\-score
@@ -58,18 +58,18 @@
.B \-l \-\^\-allcov
Report estimates for all covariates (large outputs!).
.TP
-.B \-b, \-\^\-interaction
-Which covariate to use for interaction with SNP analysis (default is no interaction, 0).
+.BI "\-b, \-\^\-interaction" " NUMBER"
+Which covariate to use for interaction with SNP analysis (default is no interaction, 0). \fINUMBER\fR indicates the column number of the covariate.
.TP
-.B \-k, \-\^\-interaction_only
+.BI "\-k, \-\^\-interaction_only" " NUMBER"
Like
.B \-\^\-interaction
-but without covariate acting in interaction with SNP (default is no interaction, 0).
+but excludes the covariate-only model term for the covariate acting in interaction with the SNP (default is no interaction, 0).
.TP
.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
+.B \-u, \-\^\-robust
Report robust (a.k.a. sandwich, a.k.a. Hubert-White) standard errors.
.TP
.B \-\^\-help
Modified: pkg/ProbABEL/src/reg1.cpp
===================================================================
--- pkg/ProbABEL/src/reg1.cpp 2014-05-27 09:56:07 UTC (rev 1746)
+++ pkg/ProbABEL/src/reg1.cpp 2014-05-27 11:38:11 UTC (rev 1747)
@@ -34,24 +34,36 @@
/**
+ * \brief Apply the genetic model to the design matrix X before
+ * running the regression.
*
+ * This also includes taking care of an interaction term if the user
+ * requested that.
*
- * if ngpreds==1 (dose data):
+ * Depending on the number of genetic predictors (ngpreds) the integer
+ * coding for the models has a different meaning:
+ *
+ * If ngpreds==1 (dose data):
* \li model 0 = additive (1 df)
*
- * if ngpreds==2 (prob data):
+ * If ngpreds==2 (prob data):
* \li model 0 = 2 df
* \li model 1 = additive (1 df)
* \li model 2 = dominant (1 df)
* \li model 3 = recessive (1 df)
* \li model 4 = over-dominant (1 df)
- * @param X Design matrix, including SNP column
- * @param model
- * @param interaction
- * @param ngpreds
- * @param is_interaction_excluded
- * @param iscox
- * @param nullmodel
+ * @param X Design matrix, including SNP column(s).
+ * @param model Integer describing the genetic model to be
+ * applied. See the list above.
+ * @param interaction Column number of the covariate used in the
+ * interaction term.
+ * @param ngpreds Number of genetic predictors (1 for dosage data, 2
+ * for probability data).
+ * @param is_interaction_excluded Indicates whether the main term for
+ * the covariate used in the interaction term should be excluded from
+ * the model.
+ * @param iscox Indicates whether a CoxPH regression is being done.
+ * @param nullmodel Indicates whether the null model is being analysed.
*
* @return Matrix with the model applied to it.
*/
@@ -75,6 +87,8 @@
{
if (interaction != 0)
{
+ // The user requested analysis with an interaction term,
+ // so ngpreds columns need to be added to the X matrix.
mematrix<double> nX;
nX.reinit(X.nrow, X.ncol + ngpreds);
int csnp_p1 = nX.ncol - 2 * ngpreds;
@@ -154,7 +168,8 @@
} // End if (interaction !=0)
else
{
- // interaction == 0
+ // No interaction analysis, no need to add/change columns
+ // to/in X.
return (X);
}
} // End: if (model == 0)
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