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| The same analyses that were originally carried for single variants should be carried out for groups of rare variants. In principle, one could simple use the presence of a rare variant (or a particular class of rare variant, such as a non-synonymous variant or a newly discovered variant) as a predictor and repeat the logistic regression, linear regression or genotype regression described above. For an initial pass, I think the precise form of this analysis is not critical, because the next step is to... | | The same analyses that were originally carried for single variants should be carried out for groups of rare variants. In principle, one could simple use the presence of a rare variant (or a particular class of rare variant, such as a non-synonymous variant or a newly discovered variant) as a predictor and repeat the logistic regression, linear regression or genotype regression described above. For an initial pass, I think the precise form of this analysis is not critical, because the next step is to... |
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− | == More Q-Q Plots === | + | == More Q-Q Plots == |
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| After carrying out initial burden tests, generate Q-Q plots for each analysis. Verify that Q-Q plots are reasonable and that genomic control value is close to 1.0. If not, refine sample and variant filters as needed. | | After carrying out initial burden tests, generate Q-Q plots for each analysis. Verify that Q-Q plots are reasonable and that genomic control value is close to 1.0. If not, refine sample and variant filters as needed. |