[Genabel-commits] r956 - pkg/GenABEL/man

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

Author: yurii
Date: 2012-09-17 12:45:56 +0200 (Mon, 17 Sep 2012)
New Revision: 956

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

Modified: pkg/GenABEL/man/GC.Rd
===================================================================
--- pkg/GenABEL/man/GC.Rd	2012-09-17 10:36:45 UTC (rev 955)
+++ pkg/GenABEL/man/GC.Rd	2012-09-17 10:45:56 UTC (rev 956)
@@ -49,6 +49,8 @@
 }
 \examples{
 data(ge03d2)
+set.seed(1)
+ge03d2 <- ge03d2[sample(1:nids(ge03d2),200),1:1000]
 qts=mlreg(phdata(ge03d2)$dm2~1,data=ge03d2,gtmode = "dominant")
 chi2.1df=results(qts)$chi2.1df
 s=summary(ge03d2)

Modified: pkg/GenABEL/man/GC_ovdom.Rd
===================================================================
--- pkg/GenABEL/man/GC_ovdom.Rd	2012-09-17 10:36:45 UTC (rev 955)
+++ pkg/GenABEL/man/GC_ovdom.Rd	2012-09-17 10:45:56 UTC (rev 956)
@@ -39,6 +39,8 @@
 }
 \examples{
 data(ge03d2)
+set.seed(1)
+ge03d2 <- ge03d2[sample(1:nids(ge03d2),200),1:1000]
 qts=mlreg(phdata(ge03d2)$dm2~1,data=ge03d2,gtmode = "overdominant")
 chi2.1df=results(qts)$chi2.1df
 s=summary(ge03d2)

Modified: pkg/GenABEL/man/findRelatives.Rd
===================================================================
--- pkg/GenABEL/man/findRelatives.Rd	2012-09-17 10:36:45 UTC (rev 955)
+++ pkg/GenABEL/man/findRelatives.Rd	2012-09-17 10:45:56 UTC (rev 956)
@@ -113,6 +113,7 @@
 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
@@ -121,5 +122,6 @@
 relInfoVS <- findRelatives(df[27:30,],q=eaf,nmeivec=c(1:6),vsIDs=idnames(df[27:30,])[1:2])
 relInfoVS
 }
+}
 \keyword{htest}
 

Modified: pkg/GenABEL/man/grammar.Rd
===================================================================
--- pkg/GenABEL/man/grammar.Rd	2012-09-17 10:36:45 UTC (rev 955)
+++ pkg/GenABEL/man/grammar.Rd	2012-09-17 10:45:56 UTC (rev 956)
@@ -51,10 +51,10 @@
 \examples{
 # Using clean ge03d2 data
 data(ge03d2.clean)
-#take half for speed
-ge03d2.clean <- ge03d2.clean[1:300,]
+#take small piece for speed
+ge03d2.clean <- ge03d2.clean[1:200,]
 # estimate genomic kinship
-gkin <- ibs(ge03d2.clean,w="freq")
+gkin <- ibs(ge03d2.clean[,sample(autosomal(ge03d2.clean),1000)],w="freq")
 # perform polygneic analysis
 h2ht <- polygenic(height ~ sex + age,kin=gkin,ge03d2.clean)
 h2ht$est
@@ -91,8 +91,7 @@
   related individuals. PLoS One. 2007 Dec 5;2(12):e1274.
 
   GRAMMAR-Gamma: Svisheva GR, Axenovich TI, Belonogova MN,
-  van Duijn CM, Aulchenko YS. Rapid variance componentsÐbased 
-  method for whole-genome association analysis
+  van Duijn CM, Aulchenko YS.
   (\link{http://dx.doi.org/10.1038/ng.2410})
 }
 \seealso{

Modified: pkg/GenABEL/man/ibs.Rd
===================================================================
--- pkg/GenABEL/man/ibs.Rd	2012-09-17 10:36:45 UTC (rev 955)
+++ pkg/GenABEL/man/ibs.Rd	2012-09-17 10:45:56 UTC (rev 956)
@@ -71,7 +71,7 @@
 }
 \examples{
 data(ge03d2c)
-
+set.seed(1)
 # compute IBS based on a random sample of 1000 autosomal marker
 selectedSnps <- sample(autosomal(ge03d2c),1000,replace=FALSE)
 a <- ibs(ge03d2c,snps=selectedSnps)
@@ -87,7 +87,7 @@
 # PAINT THE OUTLIERS IN RED
 points(mds[cl1,],pch=19,col="red")
 # compute genomic kinship matrix to be used with e.g. polygenic, mmscore, etc
-a <- ibs(ge03d2c,snps=sample(autosomal(ge03d2c),1000,replace=FALSE),weight="freq")
+a <- ibs(ge03d2c,snps=selectedSnps,weight="freq")
 a[1:5,1:5]
 # now replace diagonal with EIGENSTRAT-type of diaganal to be used for egscore
 diag(a) <- hom(ge03d2c[,autosomal(ge03d2c)])$Var
@@ -95,8 +95,8 @@
 ##############################
 # compare 'freq' with 'eVar'
 ##############################
-ibsFreq <- ibs(ge03d2c[,autosomal(ge03d2c)], weight="freq")
-ibsEvar <- ibs(ge03d2c[,autosomal(ge03d2c)], weight="eVar")
+ibsFreq <- ibs(ge03d2c,snps=selectedSnps, weight="freq")
+ibsEvar <- ibs(ge03d2c,snps=selectedSnps, weight="eVar")
 mdsEvar <- cmdscale( as.dist( 0.5 - ibsEvar ) )
 plot(mdsEvar)
 outliers <- (mdsEvar[,1]>0.1)

Modified: pkg/GenABEL/man/polygenic_hglm.Rd
===================================================================
--- pkg/GenABEL/man/polygenic_hglm.Rd	2012-09-17 10:36:45 UTC (rev 955)
+++ pkg/GenABEL/man/polygenic_hglm.Rd	2012-09-17 10:45:56 UTC (rev 956)
@@ -50,7 +50,8 @@
 }
 \examples{
 data(ge03d2ex.clean)
-df <- ge03d2ex.clean[,autosomal(ge03d2ex.clean)]
+set.seed(1)
+df <- ge03d2ex.clean[sample(1:nids(ge03d2ex.clean),200),autosomal(ge03d2ex.clean)]
 gkin <- ibs(df,w="freq")
 
 # ----- for quantitative traits

Modified: pkg/GenABEL/man/reconstructNPs.Rd
===================================================================
--- pkg/GenABEL/man/reconstructNPs.Rd	2012-09-17 10:36:45 UTC (rev 955)
+++ pkg/GenABEL/man/reconstructNPs.Rd	2012-09-17 10:45:56 UTC (rev 956)
@@ -27,7 +27,7 @@
   two parents is >2 (coded as 'NA').
 }
 \examples{
-nloci <- 1000
+nloci <- 100
 q <- runif(nloci,min=0.05,max=0.95)
 # g7---g8
 #   _|_