Population Substructure and Control Selection in Genome-Wide Association Studies
Figure 6
The conditional ranking distribution for the original PLCO prostate cancer study.
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 PC (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.