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Fig. 4 | BMC Bioinformatics

Fig. 4

From: CollapsABEL: an R library for detecting compound heterozygote alleles in genome-wide association studies

Fig. 4

GCDH analysis using a simulated phenotype. Genotype data is from Rotterdam Study (11,496 subjects and 2,744,740 SNPs after setting MAF in the interval [0.01, 0.1], and only keeping SNPs that are genotyped in every subject). Phenotype is simulated with effect size 0.7 plus a random error term from the standard normal distribution according to the collapsed genotype of two randomly selected SNPs (rs138886950 and rs10440104 in this case), and run GCDH using this as the phenotype. Genome-wide significance threshold (the red horizontal line in the figure) is set at 5.0 × 10-8 for the single-SNP approach, for GCDH (the blue horizontal line) it is set empirically at 4.5 × 10-9 by permutation analysis (see the runTypeI function in CollapsABEL). Window size is set 55. a Genome-wide scan with causal SNPs available. b Genome-wide scan without genotypes of causal SNPs. c Regional GCDH with causal SNPs available. d Regional GCDH without genotypes of causal SNPs

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BMC Bioinformatics

ISSN: 1471-2105

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