[Genabel-commits] r955 - in pkg/GenABEL: R man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Sep 17 12:36:45 CEST 2012
Author: yurii
Date: 2012-09-17 12:36:45 +0200 (Mon, 17 Sep 2012)
New Revision: 955
Modified:
pkg/GenABEL/R/GC.R
pkg/GenABEL/R/GC_ovdom.R
pkg/GenABEL/R/findRelatives.R
pkg/GenABEL/R/grammar.R
pkg/GenABEL/R/ibs.R
pkg/GenABEL/R/minimac2databel.R
pkg/GenABEL/R/polygenic_hglm.R
pkg/GenABEL/R/reconstructNPs.R
pkg/GenABEL/R/ss.R
pkg/GenABEL/man/emp.ccfast.Rd
pkg/GenABEL/man/emp.qtscore.Rd
pkg/GenABEL/man/grammar.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.R
===================================================================
--- pkg/GenABEL/R/GC.R 2012-09-14 17:54:37 UTC (rev 954)
+++ pkg/GenABEL/R/GC.R 2012-09-17 10:36:45 UTC (rev 955)
@@ -32,6 +32,8 @@
#'
#' @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/R/GC_ovdom.R
===================================================================
--- pkg/GenABEL/R/GC_ovdom.R 2012-09-14 17:54:37 UTC (rev 954)
+++ pkg/GenABEL/R/GC_ovdom.R 2012-09-17 10:36:45 UTC (rev 955)
@@ -28,6 +28,8 @@
#'
#' @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/R/findRelatives.R
===================================================================
--- pkg/GenABEL/R/findRelatives.R 2012-09-14 17:54:37 UTC (rev 954)
+++ pkg/GenABEL/R/findRelatives.R 2012-09-17 10:36:45 UTC (rev 955)
@@ -88,6 +88,7 @@
#' df <- ge03d2.clean[,autosomal(ge03d2.clean)]
#' df <- df[,sort(sample(1:nsnps(df),1000))]
#' eaf <- summary(gtdata(df))$"Q.2"
+#' \donotrun{
#' relInfo <- findRelatives(df[27:30,],q=eaf)
#' relInfo
#' # look only for 1st and 2nd degree relatives
@@ -95,6 +96,7 @@
#' relInfo1
#' relInfoVS <- findRelatives(df[27:30,],q=eaf,nmeivec=c(1:6),vsIDs=idnames(df[27:30,])[1:2])
#' relInfoVS
+#' }
#'
findRelatives <- function(gtdata,nmeivec=c(1:2),q=NULL,epsilon=0.01,
quiet=FALSE,OddsVsNull=1000,OddsVsNextBest=100,
Modified: pkg/GenABEL/R/grammar.R
===================================================================
--- pkg/GenABEL/R/grammar.R 2012-09-14 17:54:37 UTC (rev 954)
+++ pkg/GenABEL/R/grammar.R 2012-09-17 10:36:45 UTC (rev 955)
@@ -44,15 +44,15 @@
#'
#' GRAMMAR-Gamma: Svisheva GR, Axenovich TI, Belonogova MN, van Duijn CM, Aulchenko YS.
#' Rapid variance componentsÐbased method for whole-genome association analysis.
-#' (http://dx.doi.org/10.1038/ng.2410)
+#' (\link{http://dx.doi.org/10.1038/ng.2410})
#'
#' @examples
#' # Using clean ge03d2 data
#' data(ge03d2.clean)
-#' #take half for speed
-#' ge03d2.clean <- ge03d2.clean[1:300,]
+#' #take small piece for speed
+#' ge03d2.clean <- ge03d2.clean[1:200,]
#' # estimate genomic kinship
-#' gkin <- ibs(ge03d2.clean,w="freq")
+#' gkin <- ibs(ge03d2.clean[,sample(autosomal(ge03d2.clean),1000)],w="freq")
#' # perform polygneic analysis
#' h2ht <- polygenic(height ~ sex + age,kin=gkin,ge03d2.clean)
#' h2ht$est
Modified: pkg/GenABEL/R/ibs.R
===================================================================
--- pkg/GenABEL/R/ibs.R 2012-09-14 17:54:37 UTC (rev 954)
+++ pkg/GenABEL/R/ibs.R 2012-09-17 10:36:45 UTC (rev 955)
@@ -55,7 +55,7 @@
#'
#' @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)
@@ -71,7 +71,7 @@
#' # 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
@@ -79,8 +79,8 @@
#' ##############################
#' # 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/R/minimac2databel.R
===================================================================
--- pkg/GenABEL/R/minimac2databel.R 2012-09-14 17:54:37 UTC (rev 954)
+++ pkg/GenABEL/R/minimac2databel.R 2012-09-17 10:36:45 UTC (rev 955)
@@ -1,4 +1,3 @@
-#'
#' converts Minimac-imputed files to DatABEL (filevector) format
#'
#' This function converts Minimac-imputed files to \code{DatABEL} (filevector) format.
Modified: pkg/GenABEL/R/polygenic_hglm.R
===================================================================
--- pkg/GenABEL/R/polygenic_hglm.R 2012-09-14 17:54:37 UTC (rev 954)
+++ pkg/GenABEL/R/polygenic_hglm.R 2012-09-17 10:36:45 UTC (rev 955)
@@ -46,7 +46,8 @@
#'
#' @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/R/reconstructNPs.R
===================================================================
--- pkg/GenABEL/R/reconstructNPs.R 2012-09-14 17:54:37 UTC (rev 954)
+++ pkg/GenABEL/R/reconstructNPs.R 2012-09-17 10:36:45 UTC (rev 955)
@@ -23,7 +23,7 @@
#' @author Yurii Aulchenko
#'
#' @examples
-#' nloci <- 1000
+#' nloci <- 100
#' q <- runif(nloci,min=0.05,max=0.95)
#' # g7---g8
#' # _|_
Modified: pkg/GenABEL/R/ss.R
===================================================================
--- pkg/GenABEL/R/ss.R 2012-09-14 17:54:37 UTC (rev 954)
+++ pkg/GenABEL/R/ss.R 2012-09-17 10:36:45 UTC (rev 955)
@@ -366,7 +366,7 @@
}
if (!is.null(lambda(object)) & !any(names(tmp)=="Pc1df")) {
chi2.1df_corr <- tmp$chi2.1df/lambda(object)$estimate
- tmp$Pc1df <- pchisq(chi2.1df_corr, df=1, low=FALSE)
+ tmp$Pc1df <- pchisq(chi2.1df_corr, df=1, lower.tail=FALSE)
}
return(tmp)
}
Modified: pkg/GenABEL/man/emp.ccfast.Rd
===================================================================
--- pkg/GenABEL/man/emp.ccfast.Rd 2012-09-14 17:54:37 UTC (rev 954)
+++ pkg/GenABEL/man/emp.ccfast.Rd 2012-09-17 10:36:45 UTC (rev 955)
@@ -55,7 +55,8 @@
a<-ccfast("bt",data=srdta,snps=c(500:800))
plot(a)
# this does not make sense, as the whole experiment must be analysed, not a small region!
-b<-emp.ccfast("bt",data=srdta,snps=c(500:800),bcast=10)
+# also, times = 20 is way too small (should be at least 200)
+b<-emp.ccfast("bt",data=srdta,snps=c(500:800),bcast=10, times = 20)
plot(b)
# compare qvalues and empirical P
qv<-qvaluebh95(a[,"P1df"])$qval
Modified: pkg/GenABEL/man/emp.qtscore.Rd
===================================================================
--- pkg/GenABEL/man/emp.qtscore.Rd 2012-09-14 17:54:37 UTC (rev 954)
+++ pkg/GenABEL/man/emp.qtscore.Rd 2012-09-17 10:36:45 UTC (rev 955)
@@ -63,7 +63,8 @@
a<-qtscore(qt3~age+sex,data=srdta,snps=c(1:200))
plot(a)
# this does not make sense, as the whole experiment must be analysed, not a small region!
-b<-emp.qtscore(qt3~age+sex,data=srdta,snps=c(1:200))
+# also, times = 20 is way too small (should be at least 200)
+b<-emp.qtscore(qt3~age+sex,data=srdta,snps=c(1:200), times = 20)
plot(b)
}
\keyword{htest}% at least one, from doc/KEYWORDS
Modified: pkg/GenABEL/man/grammar.Rd
===================================================================
--- pkg/GenABEL/man/grammar.Rd 2012-09-14 17:54:37 UTC (rev 954)
+++ pkg/GenABEL/man/grammar.Rd 2012-09-17 10:36:45 UTC (rev 955)
@@ -91,8 +91,9 @@
related individuals. PLoS One. 2007 Dec 5;2(12):e1274.
GRAMMAR-Gamma: Svisheva GR, Axenovich TI, Belonogova MN,
- van Duijn CM, Aulchenko YS.
- (http://dx.doi.org/10.1038/ng.2410)
+ van Duijn CM, Aulchenko YS. Rapid variance componentsÐbased
+ method for whole-genome association analysis
+ (\link{http://dx.doi.org/10.1038/ng.2410})
}
\seealso{
\code{\link{polygenic}}, \code{\link{mmscore}},
Modified: pkg/GenABEL/man/scan.glm.2D.Rd
===================================================================
--- pkg/GenABEL/man/scan.glm.2D.Rd 2012-09-14 17:54:37 UTC (rev 954)
+++ pkg/GenABEL/man/scan.glm.2D.Rd 2012-09-17 10:36:45 UTC (rev 955)
@@ -54,8 +54,10 @@
\code{\link{scan.haplo.2D}}
}
\examples{
+\donotrun{
data(srdta)
a <- scan.glm.2D("bt~sex+age+CRSNP",family=binomial(),data=srdta,snps=(1:10),bcast=2)
plot(a)
}
+}
\keyword{htest}% at least one, from doc/KEYWORDS
Modified: pkg/GenABEL/man/scan.glm.Rd
===================================================================
--- pkg/GenABEL/man/scan.glm.Rd 2012-09-14 17:54:37 UTC (rev 954)
+++ pkg/GenABEL/man/scan.glm.Rd 2012-09-17 10:36:45 UTC (rev 955)
@@ -44,15 +44,19 @@
maposnp <- srdta at gtdata@map[osnp]
maposnp
reg <- snp.names(srdta,begin=maposnp-100000,end=maposnp+100000,chrom="1")
+\donotrun{
a <- scan.glm("qt3~sex+age+CRSNP",data=srdta,snps=reg)
-#plot(a)
-#plot(a,df=1)
-#add.plot(a,df=2)
+plot(a)
+plot(a,df=1)
+add.plot(a,df=2)
+}
# interaction with sex
+\donotrun{
a <- scan.glm("qt3~age+sex*CRSNP",data=srdta,snps=reg)
-#plot(a,df=1)
-#add.plot(a,df=2)
+plot(a,df=1)
+add.plot(a,df=2)
# you can do interaction with a selected polymorphisms in the same way
}
+}
\keyword{htest}% at least one, from doc/KEYWORDS
Modified: pkg/GenABEL/man/scan.haplo.2D.Rd
===================================================================
--- pkg/GenABEL/man/scan.haplo.2D.Rd 2012-09-14 17:54:37 UTC (rev 954)
+++ pkg/GenABEL/man/scan.haplo.2D.Rd 2012-09-17 10:36:45 UTC (rev 955)
@@ -54,10 +54,12 @@
}
\examples{
if (require(haplo.stats)) {
+\donotrun{
data(srdta)
c <- scan.haplo.2D("bt~sex+age+CRSNP",data=srdta,snps=(717:733),
ids=(srdta at phdata$age<40))
plot(c)
}
}
+}
\keyword{htest}% at least one, from doc/KEYWORDS
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