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Revision as of 21:22, 24 September 2012
, 21:22, 24 September 2012no edit summary
== Expected output ==
== Expected output ==
EPACTS produces a number of files and plots.
#'''test.epacts.gz''' contains all the association results.
<pre>> head test.epacts
#CHROM BEGIN END MARKER_ID NS AC CALLRATE MAF PVALUE SCORE
20 68303 68303 20:68303_A/G_Upstream:DEFB125 266 1 1 0.0018797 NA NA
20 68319 68319 20:68319_C/A_Upstream:DEFB125 266 0 1 0 NA NA
20 68396 68396 20:68396_C/T_Nonsynonymous:DEFB125 266 1 1 0.0018797 NA NA
20 76635 76635 20:76635_A/T_Intron:DEFB125 266 0 1 0 NA NA
20 76689 76689 20:76689_T/C_Synonymous:DEFB125 266 0 1 0 NA NA
20 76690 76690 20:76690_T/C_Nonsynonymous:DEFB125 266 1 1 0.0018797 NA NA
20 76700 76700 20:76700_G/A_Nonsynonymous:DEFB125 266 0 1 0 NA NA
20 76726 76726 20:76726_C/G_Nonsynonymous:DEFB125 266 0 1 0 NA NA
20 76771 76771 20:76771_C/T_Nonsynonymous:DEFB125 266 3 1 0.0056391 0.68484 0.40587
</pre>
#'''test.epacts.top5000''' contains the top 5000 associated variants ordered by p-value.
<pre>> tail test.epacts.top5000
20 56090807 56090807 20:56090807_A/G_Synonymous:CTCFL 266 112 1 0.21053 0.99754 -0.0030785
20 2560716 2560716 20:2560716_T/G_Intron:TMC2 266 68 1 0.12782 0.99755 -0.0030708
20 60885142 60885142 20:60885142_C/A_Normal_Splice_Site:LAMA5 266 215 1 0.40414 0.99757 0.0030423
20 11903654 11903654 20:11903654_G/A_Synonymous:BTBD3 266 20 1 0.037594 0.99777 -0.0027986
20 57768657 57768657 20:57768657_T/C_Synonymous:ZNF831 266 20 1 0.037594 0.99811 0.0023631
20 30037783 30037783 20:30037783_C/T_Intron:DEFB123 266 282 1 0.46992 0.99853 -0.0018438
20 61990878 61990878 20:61990878_C/T_Intron:CHRNA4 266 35 1 0.065789 0.9989 -0.0013819
20 61990939 61990939 20:61990939_G/A_Synonymous:CHRNA4 266 35 1 0.065789 0.9989 -0.0013819
20 13464030 13464030 20:13464030_C/A_Intron:TASP1 266 231 1 0.43421 0.99944 -0.00070181
20 60905717 60905717 20:60905717_T/C_Intron:LAMA5 266 471 1 0.11466 0.9995 0.00063136
</pre>
#'''test.epacts.qq.pdf''' is the QQ-plot by MAF bin.
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