[Genabel-commits] r958 - in pkg/GenABEL: R man

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

Author: yurii
Date: 2012-09-17 13:16:16 +0200 (Mon, 17 Sep 2012)
New Revision: 958

Modified:
   pkg/GenABEL/R/GC_ovdom.R
   pkg/GenABEL/R/findRelatives.R
   pkg/GenABEL/man/GC_ovdom.Rd
   pkg/GenABEL/man/findRelatives.Rd
   pkg/GenABEL/man/scan.glm.2D.Rd
   pkg/GenABEL/man/scan.glm.Rd
   pkg/GenABEL/man/scan.haplo.2D.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 11:05:11 UTC (rev 957)
+++ pkg/GenABEL/R/GC_ovdom.R	2012-09-17 11:16:16 UTC (rev 958)
@@ -35,7 +35,9 @@
 #' s=summary(ge03d2)
 #' freq=s$Q.2
 #' ### donotrun
-#' # result=GC_ovdom(p=freq,method = "median",data=chi2.1df,n=nids(ge03d2))
+#' \dontrun{
+#' 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 11:05:11 UTC (rev 957)
+++ pkg/GenABEL/R/findRelatives.R	2012-09-17 11:16:16 UTC (rev 958)
@@ -89,13 +89,15 @@
 #' 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
+#' \dontrun{
+#' 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, 

Modified: pkg/GenABEL/man/GC_ovdom.Rd
===================================================================
--- pkg/GenABEL/man/GC_ovdom.Rd	2012-09-17 11:05:11 UTC (rev 957)
+++ pkg/GenABEL/man/GC_ovdom.Rd	2012-09-17 11:16:16 UTC (rev 958)
@@ -46,7 +46,9 @@
 s=summary(ge03d2)
 freq=s$Q.2
 ### donotrun
-# result=GC_ovdom(p=freq,method = "median",data=chi2.1df,n=nids(ge03d2))
+\dontrun{
+result=GC_ovdom(p=freq,method = "median",data=chi2.1df,n=nids(ge03d2))
+}
 ### end norun
 }
 \author{

Modified: pkg/GenABEL/man/findRelatives.Rd
===================================================================
--- pkg/GenABEL/man/findRelatives.Rd	2012-09-17 11:05:11 UTC (rev 957)
+++ pkg/GenABEL/man/findRelatives.Rd	2012-09-17 11:16:16 UTC (rev 958)
@@ -114,13 +114,15 @@
 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
+\dontrun{
+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/scan.glm.2D.Rd
===================================================================
--- pkg/GenABEL/man/scan.glm.2D.Rd	2012-09-17 11:05:11 UTC (rev 957)
+++ pkg/GenABEL/man/scan.glm.2D.Rd	2012-09-17 11:16:16 UTC (rev 958)
@@ -54,7 +54,7 @@
 	\code{\link{scan.haplo.2D}}
 }
 \examples{
-\donotrun{
+\dontrun{
 data(srdta)
 a <- scan.glm.2D("bt~sex+age+CRSNP",family=binomial(),data=srdta,snps=(1:10),bcast=2)
 plot(a)

Modified: pkg/GenABEL/man/scan.glm.Rd
===================================================================
--- pkg/GenABEL/man/scan.glm.Rd	2012-09-17 11:05:11 UTC (rev 957)
+++ pkg/GenABEL/man/scan.glm.Rd	2012-09-17 11:16:16 UTC (rev 958)
@@ -44,7 +44,7 @@
 maposnp <- srdta at gtdata@map[osnp]
 maposnp
 reg <- snp.names(srdta,begin=maposnp-100000,end=maposnp+100000,chrom="1")
-\donotrun{
+\dontrun{
 a <- scan.glm("qt3~sex+age+CRSNP",data=srdta,snps=reg)
 plot(a)
 plot(a,df=1)
@@ -52,7 +52,7 @@
 }
 
 # interaction with sex
-\donotrun{
+\dontrun{
 a <- scan.glm("qt3~age+sex*CRSNP",data=srdta,snps=reg)
 plot(a,df=1)
 add.plot(a,df=2)

Modified: pkg/GenABEL/man/scan.haplo.2D.Rd
===================================================================
--- pkg/GenABEL/man/scan.haplo.2D.Rd	2012-09-17 11:05:11 UTC (rev 957)
+++ pkg/GenABEL/man/scan.haplo.2D.Rd	2012-09-17 11:16:16 UTC (rev 958)
@@ -54,7 +54,7 @@
 }
 \examples{
 if (require(haplo.stats)) {
-\donotrun{
+\dontrun{
 data(srdta)
 c <- scan.haplo.2D("bt~sex+age+CRSNP",data=srdta,snps=(717:733),
 	ids=(srdta at phdata$age<40))