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, 15:00, 24 May 2010
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| Take your dosage, geno, and info output (.dose, .geno and .info or .mldose, .mlgeno, and .mlinfo depending on non-mle or mle manner you've used) and check if dosage is the number of AL1 copies or AL2 copies. Example is given below: | | Take your dosage, geno, and info output (.dose, .geno and .info or .mldose, .mlgeno, and .mlinfo depending on non-mle or mle manner you've used) and check if dosage is the number of AL1 copies or AL2 copies. Example is given below: |
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− | ====== ======
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| | | |
− | > head -1 mldose/chr21.mldose | cut -f3 -d ' ' 1.962 > head -2 mlinfo/chr21.mlinfo SNP Al1 Al2 Freq1 MAF Quality Rsq rs885550 2 4 0.9840 0.0160 0.9682 0.0021 head -1 mlgeno/chr21.mlgeno | cut -f3 -d ' ' 2/2
| + | head -1 mldose/chr21.mldose | cut -f3 -d ' ' |
− | | + | 1.962 |
− | ====== ======
| + | head -2 mlinfo/chr21.mlinfo |
| + | SNP Al1 Al2 Freq1 MAF Quality Rsq |
| + | rs885550 2 4 0.9840 0.0160 0.9682 0.0021 |
| + | head -1 mlgeno/chr21.mlgeno | cut -f3 -d ' ' |
| + | 2/2 |
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| Based on the three files above, we've confirmed that dosage is the number of AL1 copies: you will only to check for one informative case (i.e, dosage values close to 0 or 2) since it's consistent across all individuals and all SNPs. | | Based on the three files above, we've confirmed that dosage is the number of AL1 copies: you will only to check for one informative case (i.e, dosage values close to 0 or 2) since it's consistent across all individuals and all SNPs. |