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, 12:33, 27 November 2012
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| * Enabled writing log file by defalut. (11/18/2012) | | * Enabled writing log file by defalut. (11/18/2012) |
| * Forced sample IDs to be matched when reading in kinship from a file. Perform a sanity check before reading in kinship file. If a sample of interest is not included in kinship file, then fatal error will occur. (11/19/2012) | | * Forced sample IDs to be matched when reading in kinship from a file. Perform a sanity check before reading in kinship file. If a sample of interest is not included in kinship file, then fatal error will occur. (11/19/2012) |
| + | * Added HWE pvalue in summary level statistics output. (11/27/2012) |
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| == Key Features == | | == Key Features == |
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| * prefix.traitName.singlevar.score.txt contains summary level statistics that are needed by Rare-Metal. An example is shown in below: | | * prefix.traitName.singlevar.score.txt contains summary level statistics that are needed by Rare-Metal. An example is shown in below: |
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− | LDL mean= -0.00, variance= 1.00, heritability= 34.30 | + | LDL mean= -0.00, variance= 1.00, heritability= 34.30 |
− | CHR POS REF_ALLELE ALT_ALLELE INFORMATIVE_N FOUNDER_AF ALL_AF INFORMATIVE_AC STAT ALT_ALLELE_EFFSIZE PVALUE | + | CHR POS REF_ALLELE ALT_ALLELE INFORMATIVE_N FOUNDER_AF ALL_AF INFORMATIVE_AC HWE_PVALUE STAT ALT_ALLELE_EFFSIZE PVALUE |
− | chr1 762320 G A 6103 0.0038225 0.0038225 45 4.73428 0.0949001 0.502675 | + | chr10 45410002 G A 6103 0.0341589 0.0341589 410 0.165893 126.205 0.309798 4.03074e-10 |
− | chr1 865628 G A 6103 0.00556756 0.00556756 67 18.3894 0.249333 0.0322511 | + | chr19 45412079 G A 6103 0.0368124 0.0368124 434 0.714645 -265.84 -0.587356 7.87851e-36 |
− | chr1 865665 G A 6103 8.30979e-05 8.30979e-05 1 -0.740215 -0.599493 0.505316
| + | chr19 45414451 G A 6103 0.444989 0.444989 5312 0.0759271 -26.1212 -0.00837122 0.640058 |
− | chr1 878744 C G 6103 0.00667334 0.00667334 80 -19.5138 -0.220432 0.0380796 | |
− | chr1 879381 G A 6103 8.31117e-05 8.31117e-05 1 -0.831691 -0.61887 0.473108
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| * pvalues from the above output are from the family-based single variant score test. | | * pvalues from the above output are from the family-based single variant score test. |