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| 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. |
− | #'''test.epacts.gz''' contains all the association results.
| |
| <pre>> head test.epacts | | <pre>> head test.epacts |
| #CHROM BEGIN END MARKER_ID NS AC CALLRATE MAF PVALUE SCORE | | #CHROM BEGIN END MARKER_ID NS AC CALLRATE MAF PVALUE SCORE |
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| 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> | + | </pre> 2. '''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>$ head out/test.single.b.score.epacts.top5000 |
− | <pre>> tail test.epacts.top5000 | + | #CHROM BEGIN END MARKER_ID NS AC CALLRATE MAF PVALUE SCORE |
− | 20 56090807 56090807 20:56090807_A/G_Synonymous:CTCFL 266 112 1 0.21053 0.99754 -0.0030785 | + | 20 1610894 1610894 20:1610894_G/A_Synonymous:SIRPG 266 136 1 0.25564 0.0001097 3.8681 |
− | 20 2560716 2560716 20:2560716_T/G_Intron:TMC2 266 68 1 0.12782 0.99755 -0.0030708 | + | 20 4162411 4162411 20:4162411_T/C_Intron:SMOX 266 204 1 0.38346 0.00055585 -3.4523 |
− | 20 60885142 60885142 20:60885142_C/A_Normal_Splice_Site:LAMA5 266 215 1 0.40414 0.99757 0.0030423 | + | 20 34061918 34061918 20:34061918_T/C_Intron:CEP250 266 39 1 0.073308 0.0011231 3.2577 |
− | 20 11903654 11903654 20:11903654_G/A_Synonymous:BTBD3 266 20 1 0.037594 0.99777 -0.0027986 | + | 20 4155948 4155948 20:4155948_G/A_Intron:SMOX 266 215 1 0.40414 0.0020791 -3.0787 |
− | 20 57768657 57768657 20:57768657_T/C_Synonymous:ZNF831 266 20 1 0.037594 0.99811 0.0023631 | + | 20 4680251 4680251 20:4680251_A/G_Nonsynonymous:PRNP 266 186 1 0.34962 0.0025962 3.0119 |
− | 20 30037783 30037783 20:30037783_C/T_Intron:DEFB123 266 282 1 0.46992 0.99853 -0.0018438 | + | 20 36668874 36668874 20:36668874_G/A_Synonymous:RPRD1B 266 96 1 0.18045 0.003031 2.9646 |
− | 20 61990878 61990878 20:61990878_C/T_Intron:CHRNA4 266 35 1 0.065789 0.9989 -0.0013819 | + | 20 36641871 36641871 20:36641871_G/A_Synonymous:TTI1 266 10 1 0.018797 0.004308 -2.8547 |
− | 20 61990939 61990939 20:61990939_G/A_Synonymous:CHRNA4 266 35 1 0.065789 0.9989 -0.0013819 | + | 20 32664926 32664926 20:32664926_G/A_Nonsynonymous:RALY 266 20 1 0.037594 0.0046365 2.8313 |
− | 20 13464030 13464030 20:13464030_C/A_Intron:TASP1 266 231 1 0.43421 0.99944 -0.00070181 | + | 20 34288854 34288854 20:34288854_C/T_Utr3:ROMO1 266 28 1 0.052632 0.0047722 2.822 |
− | 20 60905717 60905717 20:60905717_T/C_Intron:LAMA5 266 471 1 0.11466 0.9995 0.00063136
| + | </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]] |
| + | |
| + | 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. |
| | | |
− | </pre>
| + | [[Image:Test b score epacts mh.png]] |
− | $ 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
| + | 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> |
− | [[Image:Test b score epacts qq.png]]
| |
− | Manhattan Plot of Test Statistics<br>The file out/test.b.score.epacts.mh.pdf will be generated for chr20 only.
| |
− | [[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> | |