Population Substructure and Control Selection in Genome-Wide Association Studies
Figure 7
The conditional ranking distribution for the reconstructed prostate cancer study using external controls.
Each plot shows the histogram of ranks according to the test without PC adjustment for SNPs ranked within a given range by the test with the adjustment for the 1st, 2nd, and 4th PCs (chosen by the proposed permutation procedure). The ranking ranges (%) are shown on the horizontal axis. The frequencies (%) are shown on the vertical axis. A) The histogram of ranks for SNPs ranked in the top 0–1% by the test with PC adjustment. B) The histogram of ranks for SNPs ranked in the top 1–2% by the test with PC adjustment. C) The histogram of ranks for SNPs ranked in the top 2–3% by the test with PC adjustment. D) The histogram of ranks for SNPs ranked in the top 3–4% by the test with PC adjustment. E) The histogram of ranks for SNPs ranked in the top 4–5% by the test with PC adjustment.