srdta: GWA-type data on small region
In GenABEL.data: Data Used by the GenABEL Examples and Test Functions
Description
Usage
Format
Examples
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
1
Format
Standard object of class gwaa.data-class (see the GenABEL manual).
Examples
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#\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)
GenABEL.data documentation built on May 2, 2019, 5:48 p.m.
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Description Usage Format Examples
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
1 |
Format
Standard object of class gwaa.data-class (see the GenABEL manual).
Examples
1 2 3 4 5 6 7 8 9 10 11 12 | #\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)
|
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Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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