GenABEL.data (version 1.0.0)

srdta: GWA-type data on small region

Description

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 gwaa.data-class (see the GenABEL manual).

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)