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Revision as of 21:23, 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.
#'''test.epacts.gz''' contains all the association results.
#'''test.epacts.gz''' contains all the association results.
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
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#'''test.epacts.top5000''' contains the top 5000 associated variants ordered by p-value.
#'''test.epacts.top5000''' contains the top 5000 associated variants ordered by p-value.
<pre>> tail test.epacts.top5000
<pre>> tail test.epacts.top5000
20 60905717 60905717 20:60905717_T/C_Intron:LAMA5 266 471 1 0.11466 0.9995 0.00063136
20 60905717 60905717 20:60905717_T/C_Intron:LAMA5 266 471 1 0.11466 0.9995 0.00063136
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#'''test.epacts.qq.pdf''' is the QQ-plot by MAF bin.
$ head out/test.single.b.score.epacts.top5000 <br>#CHROM BEGIN END MARKER_ID NS AC CALLRATE MAF PVALUE SCORE<br>20 1610894 1610894 20:1610894_G/A_Synonymous:SIRPG 266 136 1 0.25564 0.0001097 3.8681<br>20 4162411 4162411 20:4162411_T/C_Intron:SMOX 266 204 1 0.38346 0.00055585 -3.4523<br>20 34061918 34061918 20:34061918_T/C_Intron:CEP250 266 39 1 0.073308 0.0011231 3.2577<br>20 4155948 4155948 20:4155948_G/A_Intron:SMOX 266 215 1 0.40414 0.0020791 -3.0787<br>20 4680251 4680251 20:4680251_A/G_Nonsynonymous:PRNP 266 186 1 0.34962 0.0025962 3.0119<br>20 36668874 36668874 20:36668874_G/A_Synonymous:RPRD1B 266 96 1 0.18045 0.003031 2.9646<br>20 36641871 36641871 20:36641871_G/A_Synonymous:TTI1 266 10 1 0.018797 0.004308 -2.8547<br>20 32664926 32664926 20:32664926_G/A_Nonsynonymous:RALY 266 20 1 0.037594 0.0046365 2.8313<br>20 34288854 34288854 20:34288854_C/T_Utr3:ROMO1 266 28 1 0.052632 0.0047722 2.822
Q-Q plot of test statistics (stratified by MAF)<br>The file out/test.b.score.epacts.qq.pdf will be generated as shown below
Manhattan Plot of Test Statistics<br>The file out/test.b.score.epacts.mh.pdf will be generated for chr20 only.
An example Genome-wide manhattan plot (from a genome-wide run) will look like below<br><br>
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<br>
