[Genabel-commits] r1434 - in pkg/GenABEL: . R demo inst/unitTests man

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Fri Nov 29 09:39:50 CET 2013 

Author: maksim
Date: 2013-11-29 09:39:49 +0100 (Fri, 29 Nov 2013)
New Revision: 1434

Modified:
   pkg/GenABEL/DESCRIPTION
   pkg/GenABEL/R/grammar.R
   pkg/GenABEL/demo/ge03d2.R
   pkg/GenABEL/demo/ge03d2ex.R
   pkg/GenABEL/demo/srdtawin.R
   pkg/GenABEL/inst/unitTests/runit.descriptives.trait.R
   pkg/GenABEL/inst/unitTests/runit.exports.R
   pkg/GenABEL/inst/unitTests/runit.iterator.R
   pkg/GenABEL/inst/unitTests/runit.merge.R
   pkg/GenABEL/inst/unitTests/runit.mmscore.R
   pkg/GenABEL/inst/unitTests/runit.polygenic.R
   pkg/GenABEL/inst/unitTests/runit.polylik.R
   pkg/GenABEL/inst/unitTests/runit.recodeChromosome.R
   pkg/GenABEL/inst/unitTests/runit.strandModify.R
   pkg/GenABEL/man/HWE.show.Rd
   pkg/GenABEL/man/PGC.Rd
   pkg/GenABEL/man/VIFGC.Rd
   pkg/GenABEL/man/VIFGC_ovdom.Rd
   pkg/GenABEL/man/Xfix.Rd
   pkg/GenABEL/man/add.phdata.Rd
   pkg/GenABEL/man/add.plot.Rd
   pkg/GenABEL/man/as.character.gwaa.data.Rd
   pkg/GenABEL/man/as.character.snp.coding.Rd
   pkg/GenABEL/man/as.character.snp.data.Rd
   pkg/GenABEL/man/as.character.snp.strand.Rd
   pkg/GenABEL/man/as.data.frame.gwaa.data.Rd
   pkg/GenABEL/man/as.double.gwaa.data.Rd
   pkg/GenABEL/man/as.double.snp.data.Rd
   pkg/GenABEL/man/as.genotype.Rd
   pkg/GenABEL/man/as.genotype.gwaa.data.Rd
   pkg/GenABEL/man/as.genotype.snp.data.Rd
   pkg/GenABEL/man/as.hsgeno.Rd
   pkg/GenABEL/man/as.hsgeno.gwaa.data.Rd
   pkg/GenABEL/man/as.hsgeno.snp.data.Rd
   pkg/GenABEL/man/autosomal.Rd
   pkg/GenABEL/man/blurGenotype.Rd
   pkg/GenABEL/man/catable.Rd
   pkg/GenABEL/man/ccfast.Rd
   pkg/GenABEL/man/check.marker-class.Rd
   pkg/GenABEL/man/check.marker.Rd
   pkg/GenABEL/man/check.trait.Rd
   pkg/GenABEL/man/cocohet.Rd
   pkg/GenABEL/man/crnames.Rd
   pkg/GenABEL/man/del.phdata.Rd
   pkg/GenABEL/man/descriptives.marker.Rd
   pkg/GenABEL/man/descriptives.scan.Rd
   pkg/GenABEL/man/descriptives.trait.Rd
   pkg/GenABEL/man/dprfast.Rd
   pkg/GenABEL/man/egscore.Rd
   pkg/GenABEL/man/emp.ccfast.Rd
   pkg/GenABEL/man/emp.qtscore.Rd
   pkg/GenABEL/man/estlambda.Rd
   pkg/GenABEL/man/export.impute.Rd
   pkg/GenABEL/man/findRelatives.Rd
   pkg/GenABEL/man/formetascore.Rd
   pkg/GenABEL/man/getLogLikelihoodGivenRelation.Rd
   pkg/GenABEL/man/grammar.Rd
   pkg/GenABEL/man/gwaa.data-class.Rd
   pkg/GenABEL/man/hom.Rd
   pkg/GenABEL/man/hom.old.Rd
   pkg/GenABEL/man/ibs.Rd
   pkg/GenABEL/man/ibs.old.Rd
   pkg/GenABEL/man/merge.gwaa.data.Rd
   pkg/GenABEL/man/merge.snp.data.Rd
   pkg/GenABEL/man/mlreg.Rd
   pkg/GenABEL/man/mlreg.p.Rd
   pkg/GenABEL/man/mmscore.Rd
   pkg/GenABEL/man/patch_strand.Rd
   pkg/GenABEL/man/perid.summary.Rd
   pkg/GenABEL/man/plot.check.marker.Rd
   pkg/GenABEL/man/plot.scan.gwaa.2D.Rd
   pkg/GenABEL/man/plot.scan.gwaa.Rd
   pkg/GenABEL/man/polygenic.Rd
   pkg/GenABEL/man/polygenic_hglm.Rd
   pkg/GenABEL/man/qtscore.Rd
   pkg/GenABEL/man/qvaluebh95.Rd
   pkg/GenABEL/man/r2fast.Rd
   pkg/GenABEL/man/r2fast.old.Rd
   pkg/GenABEL/man/recodeChromosome.Rd
   pkg/GenABEL/man/redundant.Rd
   pkg/GenABEL/man/rhofast.Rd
   pkg/GenABEL/man/scan.glm.2D.Rd
   pkg/GenABEL/man/scan.glm.Rd
   pkg/GenABEL/man/scan.gwaa-class.Rd
   pkg/GenABEL/man/scan.gwaa.2D-class.Rd
   pkg/GenABEL/man/scan.haplo.2D.Rd
   pkg/GenABEL/man/scan.haplo.Rd
   pkg/GenABEL/man/snp.coding-class.Rd
   pkg/GenABEL/man/snp.data-class.Rd
   pkg/GenABEL/man/snp.names.Rd
   pkg/GenABEL/man/snp.strand-class.Rd
   pkg/GenABEL/man/snp.subset.Rd
   pkg/GenABEL/man/summary.check.marker.Rd
   pkg/GenABEL/man/summary.gwaa.data.Rd
   pkg/GenABEL/man/summary.scan.gwaa.Rd
   pkg/GenABEL/man/summary.snp.data.Rd
   pkg/GenABEL/man/ztransform.Rd
Log:
Because most of the data are moved to a new package called GenABEL.data, I Added require(GenABEL.data) line every where data() calls GenABEL data.

Modified: pkg/GenABEL/DESCRIPTION
===================================================================
--- pkg/GenABEL/DESCRIPTION	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/DESCRIPTION	2013-11-29 08:39:49 UTC (rev 1434)
@@ -6,9 +6,9 @@
 Author: GenABEL project developers
 Contact: GenABEL project developers <genabel.project at gmail.com>
 Maintainer: Yurii Aulchenko <yurii at bionet.nsc.ru>
-Depends: R (>= 2.15.0), methods, MASS, utils, GenABEL.data
+Depends: R (>= 2.15.0), methods, MASS, utils
 Suggests: qvalue, genetics, haplo.stats, DatABEL (>= 0.9-0), 
-	hglm, MetABEL, PredictABEL, VariABEL, bigRR
+	hglm, MetABEL, PredictABEL, VariABEL, bigRR, GenABEL.data
 Description: a package for genome-wide association analysis between 
              quantitative or binary traits and single-nucleotide
              polymorphisms (SNPs). 

Modified: pkg/GenABEL/R/grammar.R
===================================================================
--- pkg/GenABEL/R/grammar.R	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/R/grammar.R	2013-11-29 08:39:49 UTC (rev 1434)
@@ -51,6 +51,7 @@
 #'
 #' @examples
 #' # Using clean ge03d2 data
+#' require(GenABEL.data)
 #' data(ge03d2.clean)
 #' # take only a small piece for speed
 #' ge03d2.clean <- ge03d2.clean[1:200,]

Modified: pkg/GenABEL/demo/ge03d2.R
===================================================================
--- pkg/GenABEL/demo/ge03d2.R	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/demo/ge03d2.R	2013-11-29 08:39:49 UTC (rev 1434)
@@ -7,6 +7,7 @@
 ###################
 
 ?"LOAD THE DATA"
+require(GenABEL.data)
 data(ge03d2)
 
 ?"ATTACH PHENOTYPIC DATA"
@@ -232,6 +233,7 @@
 top10 <- rownames(descriptives.scan(an4.sa,sort="Pc1df"))
 top10
 ?"TRY TO REPLICATE IN THE SMALL DATA SET"
+require(GenABEL.data)
 data(ge03d2c)
 confirm <- qtscore(dm2~sex+age,ge03d2c[,top10])
 descriptives.scan(confirm)

Modified: pkg/GenABEL/demo/ge03d2ex.R
===================================================================
--- pkg/GenABEL/demo/ge03d2ex.R	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/demo/ge03d2ex.R	2013-11-29 08:39:49 UTC (rev 1434)
@@ -7,6 +7,7 @@
 ###################
 
 ?"LOAD THE DATA"
+require(GenABEL.data)
 data(ge03d2ex)
 
 ?"ATTACH PHENOTYPIC DATA"
@@ -232,6 +233,7 @@
 top10 <- rownames(descriptives.scan(an4.sa,sort="Pc1df"))
 top10
 ?"TRY TO REPLICATE IN THE SMALL DATA SET"
+require(GenABEL.data)
 data(ge03d2c)
 confirm <- qtscore(dm2~sex+age,ge03d2c[,top10])
 descriptives.scan(confirm)

Modified: pkg/GenABEL/demo/srdtawin.R
===================================================================
--- pkg/GenABEL/demo/srdtawin.R	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/demo/srdtawin.R	2013-11-29 08:39:49 UTC (rev 1434)
@@ -1,7 +1,7 @@
 #
 # loading the data
 #
-
+require(GenABEL.data)
 data(srdta)
 
 #

Modified: pkg/GenABEL/inst/unitTests/runit.descriptives.trait.R
===================================================================
--- pkg/GenABEL/inst/unitTests/runit.descriptives.trait.R	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/inst/unitTests/runit.descriptives.trait.R	2013-11-29 08:39:49 UTC (rev 1434)
@@ -22,6 +22,7 @@
 
 test.descriptives.trait <- function()
 {
+  	require(GenABEL.data)
     data(ge03d2ex)
 # this works
     descriptives.trait(ge03d2ex,by.var=phdata(ge03d2ex)$sex)

Modified: pkg/GenABEL/inst/unitTests/runit.exports.R
===================================================================
--- pkg/GenABEL/inst/unitTests/runit.exports.R	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/inst/unitTests/runit.exports.R	2013-11-29 08:39:49 UTC (rev 1434)
@@ -22,6 +22,7 @@
 
 test.exports <- function()
 {
+  require(GenABEL.data)
   data(ge03d2.clean)
   nTestIds <- sample(c(10:min(100, nids(ge03d2.clean))), 1)
   nTestSnps <- sample(c(10:min(1000, nsnps(ge03d2.clean))), 1)
@@ -92,7 +93,8 @@
 
 test.export.merlin.bug2525 <- function()
 {
-  data(srdta)
+  require(GenABEL.data)
+	data(srdta)
   export.merlin(
     srdta[, 1:2], dpieceFun="new",
     mapfile="tmpNew.map", pedfile="tmpNew.ped", datafile="tmpNew.dat"
@@ -112,7 +114,8 @@
 
 
 test.export.merlin.bug2664 <- function() {
-  data(srdta)
+  require(GenABEL.data)
+	data(srdta)
   export.merlin(
     srdta[1:200, 1:10], dpieceFun="new",
     mapfile="tmp.s1.map", pedfile="tmp.s1.ped", datafile="tmp.s1.dat",

Modified: pkg/GenABEL/inst/unitTests/runit.iterator.R
===================================================================
--- pkg/GenABEL/inst/unitTests/runit.iterator.R	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/inst/unitTests/runit.iterator.R	2013-11-29 08:39:49 UTC (rev 1434)
@@ -20,6 +20,7 @@
 
 test.summary_snp_data <- function()
 {
+  require(GenABEL.data)
 	data(ge03d2)
 	srdta <- ge03d2 #[,autosomal(ge03d2)]
 	

Modified: pkg/GenABEL/inst/unitTests/runit.merge.R
===================================================================
--- pkg/GenABEL/inst/unitTests/runit.merge.R	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/inst/unitTests/runit.merge.R	2013-11-29 08:39:49 UTC (rev 1434)
@@ -22,6 +22,8 @@
 
 test.merge.bug1641 <- function()
 {
+	
+  require(GenABEL.data)
 	data(srdta)
 	x1 <- srdta[1:4,1]
 	x2 <- srdta[5:10, 2]
@@ -30,6 +32,7 @@
 
 test.merge.bug1676 <- function() 
 {
+  require(GenABEL.data)
 	data(srdta)
 	x1 <- srdta[1:4,1]
 	x2 <- srdta[5:10, 2]

Modified: pkg/GenABEL/inst/unitTests/runit.mmscore.R
===================================================================
--- pkg/GenABEL/inst/unitTests/runit.mmscore.R	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/inst/unitTests/runit.mmscore.R	2013-11-29 08:39:49 UTC (rev 1434)
@@ -22,6 +22,7 @@
 
 test.mmscore <- function()
 {
+  require(GenABEL.data)
 	data(ge03d2.clean)
 	dta <- ge03d2.clean[1:200,autosomal(ge03d2.clean)[1:3000]]
 	gkin <- ibs(dta[,1:2000],w="freq")

Modified: pkg/GenABEL/inst/unitTests/runit.polygenic.R
===================================================================
--- pkg/GenABEL/inst/unitTests/runit.polygenic.R	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/inst/unitTests/runit.polygenic.R	2013-11-29 08:39:49 UTC (rev 1434)
@@ -22,6 +22,7 @@
 
 test.polygenic.Bug1322 <- function()
 {
+  require(GenABEL.data)
 	data(ge03d2.clean)
 	df <- ge03d2.clean[1:200,autosomal(ge03d2.clean)]
 	gkin <- ibs(df,w="freq")
@@ -50,6 +51,7 @@
 
 test.polygenic.eigenOfRel <- function()
 {
+  require(GenABEL.data)
 	data(ge03d2.clean)
 	completeIds <- complete.cases(phdata(ge03d2.clean)[,c("height","sex","age")])
 	df <- ge03d2.clean[sample(which(completeIds),250),autosomal(ge03d2.clean)]

Modified: pkg/GenABEL/inst/unitTests/runit.polylik.R
===================================================================
--- pkg/GenABEL/inst/unitTests/runit.polylik.R	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/inst/unitTests/runit.polylik.R	2013-11-29 08:39:49 UTC (rev 1434)
@@ -22,6 +22,7 @@
 
 test.polylik <- function(tol = 2*.Machine$double.eps^0.5)
 {
+  	require(GenABEL.data)
     data(ge03d2.clean)
     df <- ge03d2.clean[1:150,autosomal(ge03d2.clean)]
     gkin <- ibs(df,w="freq")
@@ -47,4 +48,4 @@
     checkEquals(h2htNew$pgresidualY,h2htOld$pgresidualY, tolerance = tol)
     checkEquals(h2htNew$InvSigma,h2htOld$InvSigma, tolerance = tol)
     checkEquals(h2htNew$measuredIDs,h2htOld$measuredIDs, tolerance = tol)
-}
\ No newline at end of file
+}

Modified: pkg/GenABEL/inst/unitTests/runit.recodeChromosome.R
===================================================================
--- pkg/GenABEL/inst/unitTests/runit.recodeChromosome.R	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/inst/unitTests/runit.recodeChromosome.R	2013-11-29 08:39:49 UTC (rev 1434)
@@ -22,6 +22,7 @@
 
 test.recodeChromosome <- function()
 {
+  require(GenABEL.data)
 	data(ge03d2ex)
 	lst <- list("3"="X","2"=15)
 	dta0 <- chromosome(recodeChromosome(ge03d2ex,lst))
@@ -41,4 +42,4 @@
 	checkException( dta <- recodeChromosome(ge03d2ex,lst) )
 	lst <- list("1"="0","2"=c())
 	checkException( dta <- recodeChromosome(ge03d2ex,lst) )
-}
\ No newline at end of file
+}

Modified: pkg/GenABEL/inst/unitTests/runit.strandModify.R
===================================================================
--- pkg/GenABEL/inst/unitTests/runit.strandModify.R	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/inst/unitTests/runit.strandModify.R	2013-11-29 08:39:49 UTC (rev 1434)
@@ -22,6 +22,7 @@
 
 test.strandModify <- function()
 {
+  require(GenABEL.data)
 	data(ge03d2ex)
 	str <- strand(ge03d2ex)
 	dta1 <- ge03d2ex
@@ -36,4 +37,4 @@
 	checkIdentical(dta2,ge03d2ex)
 	table(strand(dta1),strand(ge03d2ex))
 	table(strand(dta2),strand(ge03d2ex))
-}
\ No newline at end of file
+}

Modified: pkg/GenABEL/man/HWE.show.Rd
===================================================================
--- pkg/GenABEL/man/HWE.show.Rd	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/man/HWE.show.Rd	2013-11-29 08:39:49 UTC (rev 1434)
@@ -26,6 +26,7 @@
 \code{\link{check.marker}}
 }
 \examples{
+require(GenABEL.data)
 data(srdta)
 mc <- check.marker(srdta,p.lev=0.01,ibs.mrk=0)
 mc$nohwe

Modified: pkg/GenABEL/man/PGC.Rd
===================================================================
--- pkg/GenABEL/man/PGC.Rd	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/man/PGC.Rd	2013-11-29 08:39:49 UTC (rev 1434)
@@ -56,6 +56,7 @@
   ks.test or group regress.
 }
 \examples{
+require(GenABEL.data)
 data(ge03d2)
 ge03d2 <- ge03d2[seq(from=1,to=nids(ge03d2),by=2),seq(from=1,to=nsnps(ge03d2),by=3)]
 qts <- mlreg(dm2~1,data=ge03d2,gtmode = "additive")

Modified: pkg/GenABEL/man/VIFGC.Rd
===================================================================
--- pkg/GenABEL/man/VIFGC.Rd	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/man/VIFGC.Rd	2013-11-29 08:39:49 UTC (rev 1434)
@@ -69,6 +69,7 @@
   and ks.test.
 }
 \examples{
+require(GenABEL.data)
 data(ge03d2)
 # truncate the data to make the example faster
 ge03d2 <- ge03d2[seq(from=1,to=nids(ge03d2),by=2),seq(from=1,to=nsnps(ge03d2),by=3)]

Modified: pkg/GenABEL/man/VIFGC_ovdom.Rd
===================================================================
--- pkg/GenABEL/man/VIFGC_ovdom.Rd	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/man/VIFGC_ovdom.Rd	2013-11-29 08:39:49 UTC (rev 1434)
@@ -51,6 +51,7 @@
   error functions: regress, median and ks.test.
 }
 \examples{
+require(GenABEL.data)
 data(ge03d2)
 # truncate the data to make the example faster
 ge03d2 <- ge03d2[seq(from=1,to=nids(ge03d2),by=2),seq(from=1,to=nsnps(ge03d2),by=3)]

Modified: pkg/GenABEL/man/Xfix.Rd
===================================================================
--- pkg/GenABEL/man/Xfix.Rd	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/man/Xfix.Rd	2013-11-29 08:39:49 UTC (rev 1434)
@@ -31,6 +31,7 @@
 \code{\link{check.marker}}
 }
 \examples{
+require(GenABEL.data)
 data(ge03d2c)
 # truncate the data to make the example faster
 ge03d2c <- ge03d2c[seq(from=1,to=nids(ge03d2c),by=2),seq(from=1,to=nsnps(ge03d2c),by=2)]

Modified: pkg/GenABEL/man/add.phdata.Rd
===================================================================
--- pkg/GenABEL/man/add.phdata.Rd	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/man/add.phdata.Rd	2013-11-29 08:39:49 UTC (rev 1434)
@@ -37,6 +37,7 @@
   'name' argument
 }
 \examples{
+require(GenABEL.data)
 data(srdta)
 # take a small subset for this example
 srdta <- srdta[1:10,1:5]

Modified: pkg/GenABEL/man/add.plot.Rd
===================================================================
--- pkg/GenABEL/man/add.plot.Rd	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/man/add.plot.Rd	2013-11-29 08:39:49 UTC (rev 1434)
@@ -38,6 +38,7 @@
 	\code{\link{scan.glm.2D}}
 }
 \examples{
+require(GenABEL.data)
 data(srdta)
 a <- ccfast("bt",srdta,snps=c(1:100))
 plot(a)

Modified: pkg/GenABEL/man/as.character.gwaa.data.Rd
===================================================================
--- pkg/GenABEL/man/as.character.gwaa.data.Rd	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/man/as.character.gwaa.data.Rd	2013-11-29 08:39:49 UTC (rev 1434)
@@ -30,6 +30,7 @@
 \code{\link{as.genotype.snp.data}}
 }
 \examples{
+require(GenABEL.data)
 data(srdta)
 as.character(srdta[1:5,1:10])
 }

Modified: pkg/GenABEL/man/as.character.snp.coding.Rd
===================================================================
--- pkg/GenABEL/man/as.character.snp.coding.Rd	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/man/as.character.snp.coding.Rd	2013-11-29 08:39:49 UTC (rev 1434)
@@ -30,6 +30,7 @@
 \code{\link{as.genotype.snp.data}}
 }
 \examples{
+require(GenABEL.data)
 data(srdta)
 as.character(srdta at gtdata@coding[1:5])
 }

Modified: pkg/GenABEL/man/as.character.snp.data.Rd
===================================================================
--- pkg/GenABEL/man/as.character.snp.data.Rd	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/man/as.character.snp.data.Rd	2013-11-29 08:39:49 UTC (rev 1434)
@@ -28,6 +28,7 @@
 \code{\link{as.genotype.snp.data}}
 }
 \examples{
+require(GenABEL.data)
 data(srdta)
 as.character(srdta at gtdata[1:5,1:10])
 }

Modified: pkg/GenABEL/man/as.character.snp.strand.Rd
===================================================================
--- pkg/GenABEL/man/as.character.snp.strand.Rd	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/man/as.character.snp.strand.Rd	2013-11-29 08:39:49 UTC (rev 1434)
@@ -30,6 +30,7 @@
 \code{\link{as.genotype.snp.data}}
 }
 \examples{
+require(GenABEL.data)
 data(srdta)
 as.character(srdta at gtdata@strand[1:5])
 }

Modified: pkg/GenABEL/man/as.data.frame.gwaa.data.Rd
===================================================================
--- pkg/GenABEL/man/as.data.frame.gwaa.data.Rd	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/man/as.data.frame.gwaa.data.Rd	2013-11-29 08:39:49 UTC (rev 1434)
@@ -28,6 +28,7 @@
 \code{\link{as.genotype.snp.data}}
 }
 \examples{
+require(GenABEL.data)
 data(srdta)
 as.data.frame(srdta[1:5,])
 }

Modified: pkg/GenABEL/man/as.double.gwaa.data.Rd
===================================================================
--- pkg/GenABEL/man/as.double.gwaa.data.Rd	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/man/as.double.gwaa.data.Rd	2013-11-29 08:39:49 UTC (rev 1434)
@@ -31,6 +31,7 @@
 \code{\link{as.genotype.snp.data}}
 }
 \examples{
+require(GenABEL.data)
 data(srdta)
 as.double(srdta[1:5,1:10])
 }

Modified: pkg/GenABEL/man/as.double.snp.data.Rd
===================================================================
--- pkg/GenABEL/man/as.double.snp.data.Rd	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/man/as.double.snp.data.Rd	2013-11-29 08:39:49 UTC (rev 1434)
@@ -27,6 +27,7 @@
 \code{\link{as.genotype.snp.data}}
 }
 \examples{
+require(GenABEL.data)
 data(srdta)
 as.double(srdta at gtdata[1:5,1:10])
 }

Modified: pkg/GenABEL/man/as.genotype.Rd
===================================================================
--- pkg/GenABEL/man/as.genotype.Rd	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/man/as.genotype.Rd	2013-11-29 08:39:49 UTC (rev 1434)
@@ -31,6 +31,7 @@
 \code{\link{as.genotype.snp.data}}
 }
 \examples{
+require(GenABEL.data)
 data(srdta)
 as.genotype(srdta at gtdata[1:5,1:10])
 }

Modified: pkg/GenABEL/man/as.genotype.gwaa.data.Rd
===================================================================
--- pkg/GenABEL/man/as.genotype.gwaa.data.Rd	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/man/as.genotype.gwaa.data.Rd	2013-11-29 08:39:49 UTC (rev 1434)
@@ -31,6 +31,7 @@
 \code{\link{as.genotype.snp.data}}
 }
 \examples{
+require(GenABEL.data)
 data(srdta)
 as.genotype(srdta[1:5,1:10])
 }

Modified: pkg/GenABEL/man/as.genotype.snp.data.Rd
===================================================================
--- pkg/GenABEL/man/as.genotype.snp.data.Rd	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/man/as.genotype.snp.data.Rd	2013-11-29 08:39:49 UTC (rev 1434)
@@ -27,6 +27,7 @@
 \code{\link{as.hsgeno}}
 }
 \examples{
+require(GenABEL.data)
 data(srdta)
 as.genotype(srdta at gtdata[1:5,1:10])
 }

Modified: pkg/GenABEL/man/as.hsgeno.Rd
===================================================================
--- pkg/GenABEL/man/as.hsgeno.Rd	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/man/as.hsgeno.Rd	2013-11-29 08:39:49 UTC (rev 1434)
@@ -28,6 +28,7 @@
 \code{\link{as.genotype.snp.data}}
 }
 \examples{
+require(GenABEL.data)
 data(srdta)
 as.hsgeno(srdta[1:5,1:3])
 as.hsgeno(srdta at gtdata[1:5,1:3])

Modified: pkg/GenABEL/man/as.hsgeno.gwaa.data.Rd
===================================================================
--- pkg/GenABEL/man/as.hsgeno.gwaa.data.Rd	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/man/as.hsgeno.gwaa.data.Rd	2013-11-29 08:39:49 UTC (rev 1434)
@@ -31,6 +31,7 @@
 \code{\link{as.genotype.snp.data}}
 }
 \examples{
+require(GenABEL.data)
 data(srdta)
 as.hsgeno(srdta[1:5,1:10])
 }

Modified: pkg/GenABEL/man/as.hsgeno.snp.data.Rd
===================================================================
--- pkg/GenABEL/man/as.hsgeno.snp.data.Rd	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/man/as.hsgeno.snp.data.Rd	2013-11-29 08:39:49 UTC (rev 1434)
@@ -27,6 +27,7 @@
 \code{\link{as.genotype.snp.data}}
 }
 \examples{
+require(GenABEL.data)
 data(srdta)
 as.hsgeno(srdta at gtdata[1:5,1:10])
 }

Modified: pkg/GenABEL/man/autosomal.Rd
===================================================================
--- pkg/GenABEL/man/autosomal.Rd	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/man/autosomal.Rd	2013-11-29 08:39:49 UTC (rev 1434)
@@ -25,6 +25,7 @@
 %}
 %\seealso{ ~~objects to See Also as \code{\link{help}}, ~~~ }
 \examples{
+	require(GenABEL.data)
 	data(ge03d2)
 	autosomal(ge03d2)[1:10]
 }

Modified: pkg/GenABEL/man/blurGenotype.Rd
===================================================================
--- pkg/GenABEL/man/blurGenotype.Rd	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/man/blurGenotype.Rd	2013-11-29 08:39:49 UTC (rev 1434)
@@ -31,6 +31,7 @@
   epsilon*(1-epsilon), and both allelel differ = epsilon^2.
 }
 \examples{
+require(GenABEL.data)
 data(srdta)
 # select 10 first SNPs
 df <- srdta[,1:10]

Modified: pkg/GenABEL/man/catable.Rd
===================================================================
--- pkg/GenABEL/man/catable.Rd	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/man/catable.Rd	2013-11-29 08:39:49 UTC (rev 1434)
@@ -31,6 +31,7 @@
 	\code{\link{perid.summary}}
 }
 \examples{
+	require(GenABEL.data)
 	data(srdta)
 	callr <- summary(srdta at gtdata)[,"CallRate"]
 	catable(callr,c(0.93,0.95,0.99))

Modified: pkg/GenABEL/man/ccfast.Rd
===================================================================
--- pkg/GenABEL/man/ccfast.Rd	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/man/ccfast.Rd	2013-11-29 08:39:49 UTC (rev 1434)
@@ -44,6 +44,7 @@
 \code{\link{scan.gwaa-class}}
 }
 \examples{
+require(GenABEL.data)
 data(srdta)
 a <- ccfast("bt",data=srdta,snps=c(1:10),ids=c(1:100))
 a

Modified: pkg/GenABEL/man/check.marker-class.Rd
===================================================================
--- pkg/GenABEL/man/check.marker-class.Rd	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/man/check.marker-class.Rd	2013-11-29 08:39:49 UTC (rev 1434)
@@ -50,6 +50,7 @@
 \code{\link{plot.check.marker}}
 }
 \examples{
+require(GenABEL.data)
 data(srdta)
 mc <- check.marker(data=srdta at gtdata[,1:100],redundant="all",maf=0.01,
 					minconcordance=0.9,fdr=.1,ibs.mrk=0)

Modified: pkg/GenABEL/man/check.marker.Rd
===================================================================
--- pkg/GenABEL/man/check.marker.Rd	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/man/check.marker.Rd	2013-11-29 08:39:49 UTC (rev 1434)
@@ -98,6 +98,7 @@
 }
 \examples{
 # usual way
+require(GenABEL.data)
 data(ge03d2c)
 # truncate the data to make the example faster
 ge03d2c <- ge03d2c[seq(from=1,to=nids(ge03d2c),by=2),seq(from=1,to=nsnps(ge03d2c),by=2)]
@@ -115,6 +116,7 @@
 # ready to use fixed1 for analysis
 
 # let us look into redundancy
+require(GenABEL.data)
 data(srdta)
 mc <- check.marker(data=srdta,ids=c(1:300),call=.92,perid.call=.92)
 names(mc)

Modified: pkg/GenABEL/man/check.trait.Rd
===================================================================
--- pkg/GenABEL/man/check.trait.Rd	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/man/check.trait.Rd	2013-11-29 08:39:49 UTC (rev 1434)
@@ -39,6 +39,7 @@
 	\code{\link{check.marker}}
 }
 \examples{
+require(GenABEL.data)
 data(srdta)
 check.trait("qt3",data=srdta)
 n <- names(srdta at phdata)

Modified: pkg/GenABEL/man/cocohet.Rd
===================================================================
--- pkg/GenABEL/man/cocohet.Rd	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/man/cocohet.Rd	2013-11-29 08:39:49 UTC (rev 1434)
@@ -71,6 +71,7 @@
   choosen in the input parameter test is performed.
 }
 \examples{
+require(GenABEL.data)
 data(srdta)
 chis2_nocorrection <- cocohet(data=gtdata(srdta),
 trait=phdata(srdta)$bt, window=3, test="CHI2")

Modified: pkg/GenABEL/man/crnames.Rd
===================================================================
--- pkg/GenABEL/man/crnames.Rd	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/man/crnames.Rd	2013-11-29 08:39:49 UTC (rev 1434)
@@ -20,6 +20,7 @@
 %\references{
 %}
 \examples{
+	require(GenABEL.data)
 	data(ge03d2ex)
 	a <- as.numeric(ge03d2ex[1:20,1:3])
 	crnames(dimnames(a),a==1)

Modified: pkg/GenABEL/man/del.phdata.Rd
===================================================================
--- pkg/GenABEL/man/del.phdata.Rd	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/man/del.phdata.Rd	2013-11-29 08:39:49 UTC (rev 1434)
@@ -21,6 +21,7 @@
   \code{\link{gwaa.data-class}}
 }
 \examples{
+require(GenABEL.data)
 data(srdta)
 phdata(srdta)[1:5,]
 srdta <- del.phdata(srdta,"qt1")

Modified: pkg/GenABEL/man/descriptives.marker.Rd
===================================================================
--- pkg/GenABEL/man/descriptives.marker.Rd	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/man/descriptives.marker.Rd	2013-11-29 08:39:49 UTC (rev 1434)
@@ -32,6 +32,7 @@
 %\seealso{
 %}
 \examples{
+	require(GenABEL.data)
 	data(srdta)
 	descriptives.marker(srdta)
 }

Modified: pkg/GenABEL/man/descriptives.scan.Rd
===================================================================
--- pkg/GenABEL/man/descriptives.scan.Rd	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/man/descriptives.scan.Rd	2013-11-29 08:39:49 UTC (rev 1434)
@@ -26,6 +26,7 @@
 %\seealso{
 %}
 \examples{
+	require(GenABEL.data)
 	data(srdta)
 	x <- qtscore(qt2,srdta)
 	descriptives.scan(x)

Modified: pkg/GenABEL/man/descriptives.trait.Rd
===================================================================
--- pkg/GenABEL/man/descriptives.trait.Rd	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/man/descriptives.trait.Rd	2013-11-29 08:39:49 UTC (rev 1434)
@@ -30,6 +30,7 @@
 %\seealso{
 %}
 \examples{
+	require(GenABEL.data)
 	data(srdta)
 	descriptives.trait(srdta)
 	descriptives.trait(srdta,by.var=srdta at phdata$sex)

Modified: pkg/GenABEL/man/dprfast.Rd
===================================================================
--- pkg/GenABEL/man/dprfast.Rd	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/man/dprfast.Rd	2013-11-29 08:39:49 UTC (rev 1434)
@@ -32,6 +32,7 @@
 \code{\link{rhofast}}
 }
 \examples{
+require(GenABEL.data)
 data(ge03d2)
 # D's using D'fast
 a <- dprfast(ge03d2,snps=c(1:10))

Modified: pkg/GenABEL/man/egscore.Rd
===================================================================
--- pkg/GenABEL/man/egscore.Rd	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/man/egscore.Rd	2013-11-29 08:39:49 UTC (rev 1434)
@@ -86,6 +86,7 @@
   This test is defined only for 1 d.f.
 }
 \examples{
+require(GenABEL.data)
 data(ge03d2c)
 #egscore with stratification
 gkin <- ibs(ge03d2c[,autosomal(ge03d2c)],w="freq")

Modified: pkg/GenABEL/man/emp.ccfast.Rd
===================================================================
--- pkg/GenABEL/man/emp.ccfast.Rd	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/man/emp.ccfast.Rd	2013-11-29 08:39:49 UTC (rev 1434)
@@ -51,6 +51,7 @@
 \code{\link{scan.gwaa-class}}
 }
 \examples{
+require(GenABEL.data)
 data(srdta)
 a<-ccfast("bt",data=srdta,snps=c(500:800))
 plot(a)

Modified: pkg/GenABEL/man/emp.qtscore.Rd
===================================================================
--- pkg/GenABEL/man/emp.qtscore.Rd	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/man/emp.qtscore.Rd	2013-11-29 08:39:49 UTC (rev 1434)
@@ -59,6 +59,7 @@
 \code{\link{scan.gwaa-class}}
 }
 \examples{
+require(GenABEL.data)
 data(srdta)
 a<-qtscore(qt3~age+sex,data=srdta,snps=c(1:200))
 plot(a)

Modified: pkg/GenABEL/man/estlambda.Rd
===================================================================
--- pkg/GenABEL/man/estlambda.Rd	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/man/estlambda.Rd	2013-11-29 08:39:49 UTC (rev 1434)
@@ -45,6 +45,7 @@
   fit by use of Kolmogorov-Smirnov test)
 }
 \examples{
+require(GenABEL.data)
 data(srdta)
 pex <- summary(gtdata(srdta))[,"Pexact"]
 estlambda(pex, plot=TRUE)

Modified: pkg/GenABEL/man/export.impute.Rd
===================================================================
--- pkg/GenABEL/man/export.impute.Rd	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/man/export.impute.Rd	2013-11-29 08:39:49 UTC (rev 1434)
@@ -44,6 +44,7 @@
 }
 \examples{
 \dontrun{
+require(GenABEL.data)
 data(srdta)
 export.impute(srdta[1:50,1:3])
 }

Modified: pkg/GenABEL/man/findRelatives.Rd
===================================================================
--- pkg/GenABEL/man/findRelatives.Rd	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/man/findRelatives.Rd	2013-11-29 08:39:49 UTC (rev 1434)
@@ -109,6 +109,7 @@
   parameter.
 }
 \examples{
+require(GenABEL.data)
 data(ge03d2.clean)
 df <- ge03d2.clean[,autosomal(ge03d2.clean)]
 df <- df[,sort(sample(1:nsnps(df),1000))]

Modified: pkg/GenABEL/man/formetascore.Rd
===================================================================
--- pkg/GenABEL/man/formetascore.Rd	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/man/formetascore.Rd	2013-11-29 08:39:49 UTC (rev 1434)
@@ -56,6 +56,7 @@
 %}
 \seealso{\code{\link{ztransform}},\code{\link{qtscore}}}
 \examples{
+	require(GenABEL.data)
 	data(ge03d2c)
 	x <- formetascore(bmi ~ sex+age,ge03d2c)
 	x[1:10,]

Modified: pkg/GenABEL/man/getLogLikelihoodGivenRelation.Rd
===================================================================
--- pkg/GenABEL/man/getLogLikelihoodGivenRelation.Rd	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/man/getLogLikelihoodGivenRelation.Rd	2013-11-29 08:39:49 UTC (rev 1434)
@@ -21,6 +21,7 @@
   returned with 'makeTransitionMatrix').
 }
 \examples{
+require(GenABEL.data)
 data(srdta)
 # select 10 first SNPs
 df <- srdta[,1:10]

Modified: pkg/GenABEL/man/grammar.Rd
===================================================================
--- pkg/GenABEL/man/grammar.Rd	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/man/grammar.Rd	2013-11-29 08:39:49 UTC (rev 1434)
@@ -50,6 +50,7 @@
 }
 \examples{
 # Using clean ge03d2 data
+require(GenABEL.data)
 data(ge03d2.clean)
 # take only a small piece for speed
 ge03d2.clean <- ge03d2.clean[1:200,]

Modified: pkg/GenABEL/man/gwaa.data-class.Rd
===================================================================
--- pkg/GenABEL/man/gwaa.data-class.Rd	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/man/gwaa.data-class.Rd	2013-11-29 08:39:49 UTC (rev 1434)
@@ -49,6 +49,7 @@
 	\code{\link{snp.mx-class}}
 }
 \examples{
+require(GenABEL.data)
 data(srdta)
 srdta at phdata[1:10,]
 srdta at gtdata[1:10,1:12]

Modified: pkg/GenABEL/man/hom.Rd
===================================================================
--- pkg/GenABEL/man/hom.Rd	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/man/hom.Rd	2013-11-29 08:39:49 UTC (rev 1434)
@@ -83,6 +83,7 @@
   when estimating inbreeding/variance from marker data.
 }
 \examples{
+require(GenABEL.data)
 data(ge03d2)
 h <- hom(ge03d2[,c(1:100)])
 h[1:5,]

Modified: pkg/GenABEL/man/hom.old.Rd
===================================================================
--- pkg/GenABEL/man/hom.old.Rd	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/man/hom.old.Rd	2013-11-29 08:39:49 UTC (rev 1434)
@@ -63,6 +63,7 @@
 \code{\link{snp.data-class}}
 }
 \examples{
+require(GenABEL.data)
 data(ge03d2)
 h <- hom(ge03d2[,c(1:100)])
 homsem <- h[,"Hom"]*(1-h[,"Hom"])/h[,"NoMeasured"]

Modified: pkg/GenABEL/man/ibs.Rd
===================================================================
--- pkg/GenABEL/man/ibs.Rd	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/man/ibs.Rd	2013-11-29 08:39:49 UTC (rev 1434)
@@ -79,6 +79,7 @@
   people.
 }
 \examples{
+require(GenABEL.data)
 data(ge03d2c)
 set.seed(7)
 # compute IBS based on a random sample of 1000 autosomal marker

Modified: pkg/GenABEL/man/ibs.old.Rd
===================================================================
--- pkg/GenABEL/man/ibs.old.Rd	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/man/ibs.old.Rd	2013-11-29 08:39:49 UTC (rev 1434)
@@ -55,6 +55,7 @@
 \code{\link{snp.data-class}}
 }
 \examples{
+require(GenABEL.data)
 data(ge03d2c)
 a <- ibs(data=ge03d2c,ids=c(1:10),snps=c(1:1000))
 a

Modified: pkg/GenABEL/man/merge.gwaa.data.Rd
===================================================================
--- pkg/GenABEL/man/merge.gwaa.data.Rd	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/man/merge.gwaa.data.Rd	2013-11-29 08:39:49 UTC (rev 1434)
@@ -32,6 +32,7 @@
 	\code{\link{add.phdata}}
 }
 \examples{
+	require(GenABEL.data)
 	data(srdta)
 	x1 <- srdta[c(1,3,5,6),c(2,4,5,6)]
 	x2 <- srdta[c(2,4,5,6),c(1,3,5,6)]

Modified: pkg/GenABEL/man/merge.snp.data.Rd
===================================================================
--- pkg/GenABEL/man/merge.snp.data.Rd	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/man/merge.snp.data.Rd	2013-11-29 08:39:49 UTC (rev 1434)
@@ -76,6 +76,7 @@
 	\code{\link{add.phdata}}
 }
 \examples{
+	require(GenABEL.data)
 	data(srdta)
 	x1 <- srdta[c(1,3,5,6),c(2,4,5,6)]@gtdata
 	x2 <- srdta[c(2,4,5,6),c(1,3,5,6)]@gtdata

Modified: pkg/GenABEL/man/mlreg.Rd
===================================================================
--- pkg/GenABEL/man/mlreg.Rd	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/man/mlreg.Rd	2013-11-29 08:39:49 UTC (rev 1434)
@@ -44,6 +44,7 @@
 \code{\link{qtscore}}
 }
 \examples{
+	require(GenABEL.data)
 	data(ge03d2)
 	dta <- ge03d2[,1:100]
 # analysis using linear model

Modified: pkg/GenABEL/man/mlreg.p.Rd
===================================================================
--- pkg/GenABEL/man/mlreg.p.Rd	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/man/mlreg.p.Rd	2013-11-29 08:39:49 UTC (rev 1434)
@@ -41,6 +41,7 @@
 \code{\link{qtscore}}
 }
 \examples{
+	require(GenABEL.data)
 	data(ge03d2)
 	dta <- ge03d2[,1:100]
 # analysis using linear model

Modified: pkg/GenABEL/man/mmscore.Rd
===================================================================
--- pkg/GenABEL/man/mmscore.Rd	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/man/mmscore.Rd	2013-11-29 08:39:49 UTC (rev 1434)
@@ -72,6 +72,7 @@
 \examples{
 # ge03d2 is rather bad data set to demonstrate, 
 # because this is a population-based study
+require(GenABEL.data)
 data(ge03d2.clean)
 #take half for speed
 ge03d2.clean <- ge03d2.clean[1:100,]

Modified: pkg/GenABEL/man/patch_strand.Rd
===================================================================
--- pkg/GenABEL/man/patch_strand.Rd	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/man/patch_strand.Rd	2013-11-29 08:39:49 UTC (rev 1434)
@@ -28,6 +28,7 @@
 %	\code{\link{export.merlin}}.
 %}
 \examples{
+require(GenABEL.data)
 data(srdta)
 as.character(srdta at gtdata@strand[1:20])
 a <- patch_strand(srdta,srdta at gtdata@snpnames[1:10],rep("+",10))

Modified: pkg/GenABEL/man/perid.summary.Rd
===================================================================
--- pkg/GenABEL/man/perid.summary.Rd	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/man/perid.summary.Rd	2013-11-29 08:39:49 UTC (rev 1434)
@@ -35,6 +35,7 @@
 \code{\link{snp.data-class}}
 }
 \examples{
+require(GenABEL.data)
 data(ge03d2c)
 a <- perid.summary(data=ge03d2c,snps=c(1:100),ids=c(1:10))
 a

Modified: pkg/GenABEL/man/plot.check.marker.Rd
===================================================================
--- pkg/GenABEL/man/plot.check.marker.Rd	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/man/plot.check.marker.Rd	2013-11-29 08:39:49 UTC (rev 1434)
@@ -38,6 +38,7 @@
 	\code{\link{snp.subset}}
 }
 \examples{
+require(GenABEL.data)
 data(srdta)
 mc <- check.marker(data=srdta at gtdata[,1:100],redundant="all",maf=0.01,
 					minconcordance=0.9,fdr=.1,ibs.mrk=0)

Modified: pkg/GenABEL/man/plot.scan.gwaa.2D.Rd
===================================================================
--- pkg/GenABEL/man/plot.scan.gwaa.2D.Rd	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/man/plot.scan.gwaa.2D.Rd	2013-11-29 08:39:49 UTC (rev 1434)
@@ -33,6 +33,7 @@
 	\code{\link{scan.haplo.2D}}
 }
 \examples{
+require(GenABEL.data)
 data(srdta)
 a <- scan.glm.2D("qt3~CRSNP",data=srdta,snps=c(1:10))
 # "allelic" results

Modified: pkg/GenABEL/man/plot.scan.gwaa.Rd
===================================================================
--- pkg/GenABEL/man/plot.scan.gwaa.Rd	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/man/plot.scan.gwaa.Rd	2013-11-29 08:39:49 UTC (rev 1434)
@@ -42,6 +42,7 @@
 	\code{\link{scan.haplo}}
 }
 \examples{
+require(GenABEL.data)
 data(srdta)
 a <- qtscore(bt,srdta,snps=c(1:250))
 plot(a)

Modified: pkg/GenABEL/man/polygenic.Rd
===================================================================
--- pkg/GenABEL/man/polygenic.Rd	2013-11-28 19:48:57 UTC (rev 1433)
+++ pkg/GenABEL/man/polygenic.Rd	2013-11-29 08:39:49 UTC (rev 1434)
@@ -178,6 +178,7 @@
 }
 \examples{
 # note that procedure runs on CLEAN data
+require(GenABEL.data)
 data(ge03d2ex.clean)
 gkin <- ibs(ge03d2ex.clean,w="freq")
 h2ht <- polygenic(height ~ sex + age, kin=gkin, ge03d2ex.clean)

[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/genabel -r 1434

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