This function takes a list of SNPs and searches for them in 502 European samples from 1000 Genomes phase 3 data. It then creates an LD matrix of r values (signed, and not squared). All LD values are with respect to the major alleles in the 1000G dataset. You can specify whether the allele names are displayed.

ld_matrix(snps, with_alleles = TRUE, pop = "EUR")

Arguments

snps

List of SNPs.

with_alleles

Whether to append the allele names to the SNP names. The default is TRUE.

pop

Super-population to use as reference panel. Default = "EUR". Options are EUR, SAS, EAS, AFR, AMR. 'legacy' also available - which is a previously used verison of the EUR panel with a slightly different set of markers

Value

Matrix of LD r values