Clumping
Enwu Liu
2023-09-07
Clumping is a procedure in which only the most significant SNP (i.e., the one with the lowest p-value) within each LD block is identified and chosen for further analysis. This process decreases the correlation among the remaining SNPs while preserving those SNPs with the most robust statistical support.
Here is the clumping procedure by the plink
“The clumping procedure takes all SNPs that are significant at threshold p1 that have not already been clumped (denoting these as index SNPs) and forms clumps of all other SNPs that are within a certain kb distance from the index SNP (default 250kb) and that are in linkage disequilibrium with the index SNP, based on an r-squared threshold (default 0.50)”
https://zzz.bwh.harvard.edu/plink/tutorial.shtml
Here is a figure for LD block from the paper: Zhang, Yang, et al. “Replication of association between schizophrenia and chromosome 6p21-6p22. 1 polymorphisms in Chinese Han population.” PLoS One 8.2 (2013): e56732.
How to calculate \(D'\) and \(r^2\)