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Revision as of 08:36, 1 July 2014
, 08:36, 1 July 2014→Single Variant Association Analysis
View QQ plots
View QQ plots
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:<pre>evince $OUT/assoc/single.epacts.qq.pdf&</pre>
[[File:Single.epacts.qq.png]]
[[File:Single.epacts.qq.png]]
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View Manhattan plots
View Manhattan plots
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[[File:Single.epacts.mh.png]]
:<pre>evince $OUT/assoc/single.epacts.mh.pdf&</pre>
[[File:Single.epacts.mh.png|900px]]
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View Zoom Plots
View Zoom Plots
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:<pre>evince $OUT/assoc/single.zoom.22.36995620.pdf&</pre>
[[File:Single.zoom.22.36995620.png]]
[[File:Single.zoom.22.36995620.png]]
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And run EMMAX test specifying the kinship matrix
And run EMMAX test specifying the kinship matrix
$EPACTS/bin/epacts-single --ped $IN/assoc/seqshop.ped --vcf $OUT/assoc/snps.anno.vcf.gz --out $OUT/assoc/emmax --region 22:36000000-37000000 --test q.emmax --pheno PHENO --run 2 --kinf $OUT/assoc/snps.anno.kinf
$EPACTS/bin/epacts-single --ped $SS/assoc/seqshop.ped --vcf $OUT/assoc/snps.anno.vcf.gz --out $OUT/assoc/emmax --region 22:36000000-37000000 --test q.emmax --pheno PHENO --run 2 --kinf $OUT/assoc/snps.anno.kinf
Then the results may look similar to previous ones.
Then the results may look similar to previous ones.
