GWA Test Driver

Simulated Data

Genomewide p-values are simulated as a mixture of Uniform distribution (for SNPs with no effect) and Beta distribution (for SNPs with true effects) with parameters α and β.

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Simulated Dataset #1

In these simulated data for 2000 individuals, we assumed 99% of genome-wide SNPs to be non-causal SNPs (i.e. under Null hypothesis with heritability=0) with their association p-values Uniformly distributed and remaining 1% SNPs to be causal SNPs with their heritability between 0 and 0.01 and distribution shape as Beta(0.5, 1.5).

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Simulated Dataset #2

In these simulated data for 2000 individuals, we assumed 99% of genome-wide SNPs to be non-causal SNPs (i.e. under Null hypothesis with heritability=0) with their association p-values Uniformly distributed and remaining 1% SNPs to be causal SNPs with their heritability between 0 and 0.05 and distribution shape as Beta(0.5, 1.5).

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Simulated Dataset #3

In these simulated data for 2000 individuals, we assumed 99% of genome-wide SNPs to be non-causal SNPs (i.e. under Null hypothesis with heritability=0) with their association p-values Uniformly distributed and remaining 1% SNPs to be causal SNPs with their heritability between 0 and 0.1 and distribution shape as Beta(0.5, 1.5).

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Simulated Dataset #4

In these simulated data for 2000 individuals, we assumed 99% of genome-wide SNPs to be non-causal SNPs (i.e. under Null hypothesis with Odds Ratio=1) with their association p-values Uniformly distributed and remaining 1% SNPs to be causal SNPs with the Odds Ratio between 1.0 and 1.5 and distribution shape as Beta(0.5, 1.5).

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Simulated Dataset #5

In these simulated data for 2000 individuals, we assumed 99% of genome-wide SNPs to be non-causal SNPs (i.e. under Null hypothesis with Odds Ratio=1) with their association p-values Uniformly distributed and remaining 1% SNPs to be causal SNPs with the Odds Ratio between 1.0 and 2.0 and distribution shape as Beta(0.5, 1.5).

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Simulated Dataset #6

In these simulated data for 2000 individuals, we assumed 99% of genome-wide SNPs to be non-causal SNPs (i.e. under Null hypothesis with Odds Ratio=1) with their association p-values Uniformly distributed and remaining 1% SNPs to be causal SNPs with the Odds Ratio between 1.0 and 2.5 and distribution shape as Beta(0.5, 1.5).

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