Histogram of sample sizes from 654 drug-related SNPs.

<p><b>A</b>. Total sample sizes of SNPs. <b>B</b>. Sample size of each population of SNPs. CHB and JPT are plotted separately according to the format of the original HapMap Data. SNPs with larger sample sizes are included in Phase III, and SNPs with smaller sample sizes are included in Phase II.</p

Sensitivities (%) of each measure from simulation data under H₀:<i>d</i> = 0.05,0.1…,0.3 due to an increase in sample size (Scenario I).

<p><b>A</b>. (<i>n</i>₁,<i>n</i>₂,<i>n</i>₃) = (100,100,100). <b>B</b>. (<i>n</i>₁,<i>n</i>₂,<i>n</i>₃) = (200,200,200). <b>C</b>. (<i>n</i>₁,<i>n</i>₂,<i>n</i>₃) = (100,100,100). Blue line: chi-square test; red line: F_st; black dotted line: ANOVA F-test; green dotted line: SS_d from NSCM.</p

Q-values and fold enrichments of significant terms in HD group.

<p>FE: Fold enrichment</p><p>BH’s q: Benjamini-Hochberg’s q-value</p><p>Q-values and fold enrichments of significant terms in HD group.</p

Specificities (%) of each measure from simulation data under H₀:<i>d</i> = 0 due to an increase in sample size (Scenario I).

<p>The chi-square test and ANOVA F-test are similar, and F_st and SS_d from NSCM are nearly identical. Blue line: chi-square test; red line: F_st; black dotted line: ANOVA F-test; green dotted line: SS_d from NSCM.</p

Sensitivities (%) of each measure from simulation data under H₀:<i>d</i>=0.05,0.1…,0.3 due to bias in sample size (Scenario II).

<p>A. (<i>n</i>₁,<i>n</i>₂,<i>n</i>₃) = (200,100,100). <b>B</b>. (<i>n</i>₁,<i>n</i>₂,<i>n</i>₃) = (100,200,100). <b>C</b>. (<i>n</i>₁,<i>n</i>₂,<i>n</i>₃) = (100,100,200). Blue line: chi-square test; red line: F_st; black dotted line: ANOVA F-test; green dotted line: SS_d from NSCM.</p

Summary of each SNP group.

<p>Summary of each SNP group.</p

Boxplots representing four measures of simulation data with an increase in <i>d</i>.

<p><b>A.</b> Variation of distributions due to increase in sample sizes (Case I). <b>B.</b> Variation of distributions due to bias of sample sizes (Case II). For both cases, the <i>x</i>-axis denotes the distance <i>d</i>, and the <i>y</i>-axis and denotes the following measures: -log₁₀<i>Pvalue</i> for chi-square test and ANOVA F-test; Weir and Cockerham’s F_st estimates for F_st; </p><p></p><p></p><p></p><p></p><p><mo>∑</mo></p><mo>​</mo><p></p><p><mi>d</mi><mi>i</mi><mn>2</mn></p><p></p><p></p><p></p> for NSCM.<p></p