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SEQPower Exercise - Revision history
2026-04-05T20:08:17Z
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Serveradmin: Created page with "__NOTITLE__ ==SEQPower== spower -h<br /> spower LOGIT -h<br /> spower LOGIT Kryukov2009European1800.sfs --sample_size 1000 --OR_rare_detrimental 1.5 --method "CFisher --name..."
2017-02-23T18:41:18Z
<p>Created page with "__NOTITLE__ ==SEQPower== spower -h<br /> spower LOGIT -h<br /> spower LOGIT Kryukov2009European1800.sfs --sample_size 1000 --OR_rare_detrimental 1.5 --method "CFisher --name..."</p>
<p><b>New page</b></p><div>__NOTITLE__<br />
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==SEQPower==<br />
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spower -h<br /> spower LOGIT -h<br /> spower LOGIT Kryukov2009European1800.sfs --sample_size 1000 --OR_rare_detrimental 1.5 --method "CFisher --name CMC" -r 100 -j 4 -l 1 -o exercise<br /> spower show exercise.csv<br /> spower show exercise.csv power*<br /> spower show exercise.loci.csv<br /> spower show exercise.loci.csv maf<br /> spower show tests<br /> spower show test SKAT<br /> spower LOGIT Kryukov2009European1800.sfs --def_rare 0.01 --def_neutral -0.00001 0.00001 --moi A --proportion_detrimental 1 --proportion_protective 0 --OR_rare_detrimental 1.5 --OR_common_detrimental 1 --baseline_effect 0.01 --sample_size 1000 --p1 0.5 --limit 1 --alpha 0.05 --method "KBAC --name K1 --mafupper 0.01 --maflower 0 --alternative 1 --moi additive --permutations 1000 --adaptive 0.1" --replicates 1000 --jobs 4 -o exercise<br /> spower LOGIT Kryukov2009European1800.sfs --sample_size 1000 --OR_rare_detrimental 1.2 --ORmax_rare_detrimental 3.0 --method CFisher -r 100 -j 4 -l 1 -o exercise<br /> spower show exercise.loci.csv effect*<br /> spower LOGIT Kryukov2009European1800.sfs --sample_size 1000 --OR_rare_detrimental 1.2 --ORmax_rare_detrimental 3.0 --proportion_detrimental 0.8 --method CFisher -r 100 -j 4 -l 1 -o exercise<br /> spower LOGIT Kryukov2009European1800.sfs --sample_size 1000 --OR_rare_detrimental 1.5 --missing_sites 0.05 --method CFisher -r 100 -j 4 -l 1 -o exercise <br /> spower LOGIT Kryukov2009European1800.sfs --sample_size 1000 --OR_rare_detrimental 1.5 --missing_low_maf 0.000125 --method CFisher -r 100 -j 4 -l 1 -o exercise <br /> spower LOGIT Kryukov2009European1800.sfs --sample_size 1000 --OR_rare_detrimental 1.5 --method "CFisher --alternative 1 --name CMC" "KBAC --permutations 1000 --alternative 1" "WSSRankTest --alternative 1 --name WSS" "VTtest --alternative 1 --permutations 1000" "SKAT disease" -r 100 -j 4 -l 1 -o exercise<br /> spower show exercise.csv method power<br /> spower LOGIT Kryukov2009European1800.sfs --sample_size 1000 --OR_rare_detrimental 1.5 -j 1 -l 1 -o exercise<br /> spower LOGIT Kryukov2009European1800.sfs --power 0.8 --OR_rare_detrimental 1.5 -j 1 -l 1 -o exercise<br /> spower LNR Kryukov2009European1800.sfs --sample_size 1000 --meanshift_rare_detrimental 0.2 --method "CollapseQt --name CMC --alternative 2" -r 100 -j 4 -l 1 -o exercise<br /> spower LNR Kryukov2009European1800.sfs --sample_size 1000 --meanshift_rare_detrimental 0.2 --meanshiftmax_rare_detrimental 0.5 --method "CollapseQt --alternative 2" -r 100 -j 4 -l 1 -o exercise<br /> spower ELNR Kryukov2009European1800.sfs --sample_size 1000 --meanshift_rare_detrimental 0.2 --QT_thresholds 0.4 0.6 --method "CollapseQt --alternative 2" -r 100 -j 4 -l 1 -o exercise<br /> spower show exercise.csv sample* power<br />spower ELNR Kryukov2009European1800.sfs --sample_size 1000 --p1 0.5 --meanshift_rare_detrimental 0.5 --QT_thresholds 0.4 0.6 --method "CollapseQt --alternative 2" -r 100 -j 4 -l 1 -o exercise<br /> spower LOGIT Kryukov2009European1800.sfs --sample_size 1000 --OR_rare_detrimental 1.5 --method "GroupWrite ExerciseSimulation" -j 4 -o exercise -v1<br /> spower show exercise.SEQPowerDB<br /> spower show exercise.SEQPowerDB LOGIT<br /> spower show exercise.SEQPowerDB LOGIT method power title --condition "where power between 0.25 and 0.95"<br /> for i in 1 1.5 2 2.5 3 3.5 4; do<br /> spower LOGIT Kryukov2009European1800.sfs --sample_size 1000 --OR_rare_detrimental $i --method "CFisher --name CMC$i" --title FixedOR$i -r 100 -j 4 -l 1 -o exercise2<br /> done<br />spower show exercise2.SEQPowerDB LOGIT method power title</div>
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