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Revision as of 21:27, 24 September 2012
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== Expected output ==
== Expected output ==
EPACTS produces a number of files and plots.
EPACTS produces a number of files and plots.
1. '''test.epacts.gz''' contains all the association results.
1. '''test.epacts.gz''' contains all the association results.
<pre>> head test.epacts
<pre>> head test.epacts
20 76771 76771 20:76771_C/T_Nonsynonymous:DEFB125 266 3 1 0.0056391 0.68484 0.40587
20 76771 76771 20:76771_C/T_Nonsynonymous:DEFB125 266 3 1 0.0056391 0.68484 0.40587
</pre> 2. '''test.epacts.top5000''' contains the top 5000 associated variants ordered by p-value.
</pre>
2. '''test.epacts.top5000''' contains the top 5000 associated variants ordered by p-value.
<pre>$ head out/test.single.b.score.epacts.top5000
<pre>$ head out/test.single.b.score.epacts.top5000
#CHROM BEGIN END MARKER_ID NS AC CALLRATE MAF PVALUE SCORE
#CHROM BEGIN END MARKER_ID NS AC CALLRATE MAF PVALUE SCORE
20 32664926 32664926 20:32664926_G/A_Nonsynonymous:RALY 266 20 1 0.037594 0.0046365 2.8313
20 32664926 32664926 20:32664926_G/A_Nonsynonymous:RALY 266 20 1 0.037594 0.0046365 2.8313
20 34288854 34288854 20:34288854_C/T_Utr3:ROMO1 266 28 1 0.052632 0.0047722 2.822
20 34288854 34288854 20:34288854_C/T_Utr3:ROMO1 266 28 1 0.052632 0.0047722 2.822
</pre>
</pre>
3. '''test.epacts.qq.pdf''' contains the Q-Q plot of test p-values (stratified by MAF)<br>[[Image:Test b score epacts qq.png]]
3. '''test.epacts.qq.pdf''' contains the Q-Q plot of test p-values (stratified by MAF)<br>[[Image:Test b score epacts qq.png]]
4. '''test.epacts.mh.pdf''' contains the Manhattan Plot of test p-values<br>The file out/test.b.score.epacts.mh.pdf will be generated for chr20 only.
4. '''test.epacts.mh.pdf''' contains the Manhattan Plot of test p-values<br>The file out/test.b.score.epacts.mh.pdf will be generated for chr20 only.
[[Image:Test b score epacts mh.png]]
[[Image:Test b score epacts mh.png]]
An example Genome-wide manhattan plot (from a genome-wide run) will look like below<br><br> [[Image:Tes b score epacts mh gw.png]] <br>
An example Genome-wide manhattan plot (from a genome-wide run) will look like below<br><br> [[Image:Tes b score epacts mh gw.png]] <br>
