[Genabel-commits] r1430 - pkg/GenABEL/man

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

Author: maksim
Date: 2013-11-28 05:46:40 +0100 (Thu, 28 Nov 2013)
New Revision: 1430

Removed:
   pkg/GenABEL/man/ge03d2.Rd
   pkg/GenABEL/man/srdta.Rd
Log:
Moved ge03d2.Rd and srdta.Rd to GenABEL.data

Deleted: pkg/GenABEL/man/ge03d2.Rd
===================================================================
--- pkg/GenABEL/man/ge03d2.Rd	2013-11-28 04:38:54 UTC (rev 1429)
+++ pkg/GenABEL/man/ge03d2.Rd	2013-11-28 04:46:40 UTC (rev 1430)
@@ -1,55 +0,0 @@
-\name{ge03d2}
-\alias{ge03d2}
-\alias{ge03d2.clean}
-\alias{ge03d2c}
-\alias{ge03d2ex}
-\alias{ge03d2ex.clean}
-\alias{pop2.ids}
-\alias{qc.nostr}
-\alias{qc.str}
-\docType{data}
-\title{GWA-type data on few small region}
-\description{
-	\code{ge03d2} 
-	A small data set (approximately 1,000 people and 8,000 SNPs) containing 
-	data on 3 autosomes and X chromsome. Is a good set for 
-	demonatration of the QC procedures (different genotyping errors
-	are introduced) and GWA analysis. Run demo(ge03d2) to see a demo.
-	This data set was developed for the "Advances in population-
-	based studies" (Ge03) course of the Nihes.
-
-	\code{ge03d2c} 
-	A small data set (approximately 200 people and 8,000 SNPs) containing 
-	data on 3 autosomes and X chromsome. This data set is 
-	complementary to \code{\link{ge03d2}}.
-
-	\code{ge03d2ex} 
-	A small data set (approximately 150 people and 4,000 SNPs) containing 
-	data on 3 autosomes and X chromsome. Is a good set for 
-	demonatration of the QC procedures (different genotyping errors
-	are introduced) and GWA analysis. 
-	This data set was developed for the "Advances in population-
-	based studies" (Ge03) course of the Nihes.
-	See vignette "GenABEL-tutorial.pdf" for details.
-
-	The data sets with extension ".clean" are sets after QC.
-}
-\usage{data(ge03d2)}
-%\format{
-%}
-%\details{
-%}
-%\source{
-%}
-%\references{
-%}
-\examples{
-#main example: use this to see full functionality
-# demo(ge03d2)
-
-# load and work with ge03d2
-data(ge03d2)
-a <- qtscore(dm2,ge03d2)
-plot(a)
-}
-\keyword{datasets}

Deleted: pkg/GenABEL/man/srdta.Rd
===================================================================
--- pkg/GenABEL/man/srdta.Rd	2013-11-28 04:38:54 UTC (rev 1429)
+++ pkg/GenABEL/man/srdta.Rd	2013-11-28 04:46:40 UTC (rev 1430)
@@ -1,42 +0,0 @@
-\name{srdta}
-\alias{srdta}
-\docType{data}
-\title{GWA-type data on small region}
-\description{
-	\code{srdta} contains gwaa.data object with results 
-	on a small region of 
-	about 2.5 Mb. 833 SNPs are typed on 2500 people.
-	NA rate is 95\%. Sex, age, two quantitative (qt1 and 
-	qt2) and one binary (bt) traits are available for 
-	analysis. Run demo(srdta) and check tut-srdta.pdf 
-	to see examples of work with this data set. 
-	Original data files used for this set are located at 
-	YOUR\_R\_LIB\_LOCATION/exdata/srphenos.dat (phenotypes), 
-	srgenos.dat (human-readable genotypes) and srgenos.raw 
-	(genotypes in internal format)}
-\usage{data(srdta)}
-\format{
-	Standard object of class \code{\link{gwaa.data-class}}
-}
-%\details{
-%}
-%\source{
-%}
-%\references{
-%}
-\examples{
-
-\dontrun{
-demo(srdta)
-}
-
-# load and work with srdta
-data(srdta)
-# truncate the data to make the example faster
-srdta <- srdta[seq(from=1,to=nids(srdta),by=2),seq(from=1,to=nsnps(srdta),by=2)]
-mc <- check.marker(data=gtdata(srdta)[,1:100],redundant="all",
-					maf=0.01,minconcordance=0.9,fdr=.1,ibs.mrk=0)
-plot(mc)
-check.trait(names(phdata(srdta)),srdta)
-}
-\keyword{datasets}