[Genabel-commits] r939 - in pkg/GenABEL: R man

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

Author: nd_0001
Date: 2012-08-10 19:28:09 +0200 (Fri, 10 Aug 2012)
New Revision: 939

Modified:
   pkg/GenABEL/R/GC.R
   pkg/GenABEL/R/GC_ovdom.R
   pkg/GenABEL/R/PGC.R
   pkg/GenABEL/man/GC.Rd
   pkg/GenABEL/man/GC_ovdom.Rd
   pkg/GenABEL/man/PGC.Rd
Log:
Some changes in genomic control functions

Modified: pkg/GenABEL/R/GC.R
===================================================================
--- pkg/GenABEL/R/GC.R	2012-08-09 19:05:11 UTC (rev 938)
+++ pkg/GenABEL/R/GC.R	2012-08-10 17:28:09 UTC (rev 939)
@@ -31,7 +31,12 @@
 #' @author Yakov Tsepilov
 #' 
 #' @examples
-#' #Sorry, this block will appear later
+#' data(ge03d2)
+#' qts=mlreg(phdata(ge03d2)$dm2~1,data=ge03d2,gtmode = "dominant")
+#' chi2.1df=results(qts)$chi2.1df
+#' s=summary(ge03d2)
+#' freq=s$Q.2
+#' result=GC(p=freq,x=1,method = "median",CA=FALSE,data=chi2.1df,n=nids(ge03d2))
 #' 
 #' @keywords htest
 #'

Modified: pkg/GenABEL/R/GC_ovdom.R
===================================================================
--- pkg/GenABEL/R/GC_ovdom.R	2012-08-09 19:05:11 UTC (rev 938)
+++ pkg/GenABEL/R/GC_ovdom.R	2012-08-10 17:28:09 UTC (rev 939)
@@ -27,7 +27,12 @@
 #' @author Yakov Tsepilov
 #' 
 #' @examples
-#' #Sorry, this block will appear later
+#' data(ge03d2)
+#' qts=mlreg(phdata(ge03d2)$dm2~1,data=ge03d2,gtmode = "overdominant")
+#' chi2.1df=results(qts)$chi2.1df
+#' s=summary(ge03d2)
+#' freq=s$Q.2
+#' result=GC_ovdom(p=freq,method = "median",data=chi2.1df,n=nids(ge03d2))
 #' 
 #' @keywords htest
 #'

Modified: pkg/GenABEL/R/PGC.R
===================================================================
--- pkg/GenABEL/R/PGC.R	2012-08-09 19:05:11 UTC (rev 938)
+++ pkg/GenABEL/R/PGC.R	2012-08-10 17:28:09 UTC (rev 939)
@@ -24,7 +24,12 @@
 #' @author Yakov Tsepilov
 #' 
 #' @examples
-#' #It will be modified soon!
+#' data(ge03d2)
+#' qts=qtscore(phdata(ge03d2)$dm2, ge03d2)
+#' chi2.1df=results(qts)$chi2.1df
+#' s=summary(ge03d2)
+#' MAF=s$Q.2
+#' result=PGC(data=chi2.1df,method="regress",p=MAF,df=1, pol.d=3, plot=FALSE, start.corr=FALSE)
 #'
 #' @keywords htest
 #' 

Modified: pkg/GenABEL/man/GC.Rd
===================================================================
--- pkg/GenABEL/man/GC.Rd	2012-08-09 19:05:11 UTC (rev 938)
+++ pkg/GenABEL/man/GC.Rd	2012-08-10 17:28:09 UTC (rev 939)
@@ -48,7 +48,12 @@
   functions: regress, median and ks.test.
 }
 \examples{
-#Sorry, this block will appear later
+data(ge03d2)
+qts=mlreg(phdata(ge03d2)$dm2~1,data=ge03d2,gtmode = "dominant")
+chi2.1df=results(qts)$chi2.1df
+s=summary(ge03d2)
+freq=s$Q.2
+result=GC(p=freq,x=1,method = "median",CA=FALSE,data=chi2.1df,n=nids(ge03d2))
 }
 \author{
   Yakov Tsepilov

Modified: pkg/GenABEL/man/GC_ovdom.Rd
===================================================================
--- pkg/GenABEL/man/GC_ovdom.Rd	2012-08-09 19:05:11 UTC (rev 938)
+++ pkg/GenABEL/man/GC_ovdom.Rd	2012-08-10 17:28:09 UTC (rev 939)
@@ -38,7 +38,12 @@
   regress, median and ks.test.
 }
 \examples{
-#Sorry, this block will appear later
+data(ge03d2)
+qts=mlreg(phdata(ge03d2)$dm2~1,data=ge03d2,gtmode = "overdominant")
+chi2.1df=results(qts)$chi2.1df
+s=summary(ge03d2)
+freq=s$Q.2
+result=GC_ovdom(p=freq,method = "median",data=chi2.1df,n=nids(ge03d2))
 }
 \author{
   Yakov Tsepilov

Modified: pkg/GenABEL/man/PGC.Rd
===================================================================
--- pkg/GenABEL/man/PGC.Rd	2012-08-09 19:05:11 UTC (rev 938)
+++ pkg/GenABEL/man/PGC.Rd	2012-08-10 17:28:09 UTC (rev 939)
@@ -38,7 +38,12 @@
   diffrent error functions: regress, median and ks.test.
 }
 \examples{
-#It will be modified soon!
+data(ge03d2)
+qts=qtscore(phdata(ge03d2)$dm2, ge03d2)
+chi2.1df=results(qts)$chi2.1df
+s=summary(ge03d2)
+MAF=s$Q.2
+result=PGC(data=chi2.1df,method="regress",p=MAF,df=1, pol.d=3, plot=FALSE, start.corr=FALSE)
 }
 \author{
   Yakov Tsepilov