[Genabel-commits] r957 - in pkg/GenABEL: R man

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

Author: yurii
Date: 2012-09-17 13:05:11 +0200 (Mon, 17 Sep 2012)
New Revision: 957

Modified:
   pkg/GenABEL/R/GC_ovdom.R
   pkg/GenABEL/R/findRelatives.R
   pkg/GenABEL/R/grammar.R
   pkg/GenABEL/man/GC_ovdom.Rd
   pkg/GenABEL/man/findRelatives.Rd
   pkg/GenABEL/man/grammar.Rd
Log:
trying to cut the time spent in examples

Modified: pkg/GenABEL/R/GC_ovdom.R
===================================================================
--- pkg/GenABEL/R/GC_ovdom.R	2012-09-17 10:45:56 UTC (rev 956)
+++ pkg/GenABEL/R/GC_ovdom.R	2012-09-17 11:05:11 UTC (rev 957)
@@ -28,13 +28,15 @@
 #' 
 #' @examples
 #' data(ge03d2)
-#' set.seed(1)
-#' ge03d2 <- ge03d2[sample(1:nids(ge03d2),200),1:1000]
+#' set.seed(2)
+#' ge03d2 <- ge03d2[sample(1:nids(ge03d2),250),1:1500]
 #' 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))
+#' ### donotrun
+#' # result=GC_ovdom(p=freq,method = "median",data=chi2.1df,n=nids(ge03d2))
+#' ### end norun
 #' 
 #' @keywords htest
 #'

Modified: pkg/GenABEL/R/findRelatives.R
===================================================================
--- pkg/GenABEL/R/findRelatives.R	2012-09-17 10:45:56 UTC (rev 956)
+++ pkg/GenABEL/R/findRelatives.R	2012-09-17 11:05:11 UTC (rev 957)
@@ -88,15 +88,15 @@
 #' df <- ge03d2.clean[,autosomal(ge03d2.clean)]
 #' df <- df[,sort(sample(1:nsnps(df),1000))]
 #' eaf <- summary(gtdata(df))$"Q.2"
-#' \donotrun{
-#' relInfo <- findRelatives(df[27:30,],q=eaf)
-#' relInfo
-#' # look only for 1st and 2nd degree relatives
-#' relInfo1 <- findRelatives(df[27:30],q=eaf,gkinCutOff=-1,nmeivec=c(1,2,3))
-#' relInfo1
-#' relInfoVS <- findRelatives(df[27:30,],q=eaf,nmeivec=c(1:6),vsIDs=idnames(df[27:30,])[1:2])
-#' relInfoVS
-#' }
+#' ### donotrun
+#' # relInfo <- findRelatives(df[27:30,],q=eaf)
+#' # relInfo
+#' ## look only for 1st and 2nd degree relatives
+#' # relInfo1 <- findRelatives(df[27:30],q=eaf,gkinCutOff=-1,nmeivec=c(1,2,3))
+#' # relInfo1
+#' # relInfoVS <- findRelatives(df[27:30,],q=eaf,nmeivec=c(1:6),vsIDs=idnames(df[27:30,])[1:2])
+#' # relInfoVS
+#' ### end norun
 #' 
 findRelatives <- function(gtdata,nmeivec=c(1:2),q=NULL,epsilon=0.01, 
 		quiet=FALSE,OddsVsNull=1000,OddsVsNextBest=100,

Modified: pkg/GenABEL/R/grammar.R
===================================================================
--- pkg/GenABEL/R/grammar.R	2012-09-17 10:45:56 UTC (rev 956)
+++ pkg/GenABEL/R/grammar.R	2012-09-17 11:05:11 UTC (rev 957)
@@ -44,7 +44,7 @@
 #' 
 #' GRAMMAR-Gamma: Svisheva GR, Axenovich TI, Belonogova MN, van Duijn CM, Aulchenko YS. 
 #' Rapid variance componentsÐbased method for whole-genome association analysis. 
-#' (\link{http://dx.doi.org/10.1038/ng.2410})
+#' Nature Genetics. 2012 (http://dx.doi.org/10.1038/ng.2410)
 #' 
 #' @examples 
 #' # Using clean ge03d2 data 

Modified: pkg/GenABEL/man/GC_ovdom.Rd
===================================================================
--- pkg/GenABEL/man/GC_ovdom.Rd	2012-09-17 10:45:56 UTC (rev 956)
+++ pkg/GenABEL/man/GC_ovdom.Rd	2012-09-17 11:05:11 UTC (rev 957)
@@ -39,13 +39,15 @@
 }
 \examples{
 data(ge03d2)
-set.seed(1)
-ge03d2 <- ge03d2[sample(1:nids(ge03d2),200),1:1000]
+set.seed(2)
+ge03d2 <- ge03d2[sample(1:nids(ge03d2),250),1:1500]
 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))
+### donotrun
+# result=GC_ovdom(p=freq,method = "median",data=chi2.1df,n=nids(ge03d2))
+### end norun
 }
 \author{
   Yakov Tsepilov

Modified: pkg/GenABEL/man/findRelatives.Rd
===================================================================
--- pkg/GenABEL/man/findRelatives.Rd	2012-09-17 10:45:56 UTC (rev 956)
+++ pkg/GenABEL/man/findRelatives.Rd	2012-09-17 11:05:11 UTC (rev 957)
@@ -113,15 +113,15 @@
 df <- ge03d2.clean[,autosomal(ge03d2.clean)]
 df <- df[,sort(sample(1:nsnps(df),1000))]
 eaf <- summary(gtdata(df))$"Q.2"
-\\donotrun{
-relInfo <- findRelatives(df[27:30,],q=eaf)
-relInfo
-# look only for 1st and 2nd degree relatives
-relInfo1 <- findRelatives(df[27:30],q=eaf,gkinCutOff=-1,nmeivec=c(1,2,3))
-relInfo1
-relInfoVS <- findRelatives(df[27:30,],q=eaf,nmeivec=c(1:6),vsIDs=idnames(df[27:30,])[1:2])
-relInfoVS
+### donotrun
+# relInfo <- findRelatives(df[27:30,],q=eaf)
+# relInfo
+## look only for 1st and 2nd degree relatives
+# relInfo1 <- findRelatives(df[27:30],q=eaf,gkinCutOff=-1,nmeivec=c(1,2,3))
+# relInfo1
+# relInfoVS <- findRelatives(df[27:30,],q=eaf,nmeivec=c(1:6),vsIDs=idnames(df[27:30,])[1:2])
+# relInfoVS
+### end norun
 }
-}
 \keyword{htest}
 

Modified: pkg/GenABEL/man/grammar.Rd
===================================================================
--- pkg/GenABEL/man/grammar.Rd	2012-09-17 10:45:56 UTC (rev 956)
+++ pkg/GenABEL/man/grammar.Rd	2012-09-17 11:05:11 UTC (rev 957)
@@ -91,8 +91,8 @@
   related individuals. PLoS One. 2007 Dec 5;2(12):e1274.
 
   GRAMMAR-Gamma: Svisheva GR, Axenovich TI, Belonogova MN,
-  van Duijn CM, Aulchenko YS.
-  (\link{http://dx.doi.org/10.1038/ng.2410})
+  van Duijn CM, Aulchenko YS. Nature Genetics. 2012
+  (http://dx.doi.org/10.1038/ng.2410)
 }
 \seealso{
   \code{\link{polygenic}}, \code{\link{mmscore}},