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SNPair_LD

Measure pair-wise linkage disequilibrium from a VCF file. The linkage disequilibrium metrics D' and R^2 are calculated for each SNP pair in a VCF file, and statistical significance is assessed. To compensate for the large number of pairwise comparisons, p-values are FDR corrected.

Requirements

SNPair_LD.R requires the following libraries:

  • pegas
  • fields
  • genetics
  • reshape2
  • ggplot2

Usage

SNPair_LD.R <vcf_file> <output_prefix>

A complete run of SNPair_LD.R will produce the following output files:

  • <prefix>_Dc.pdf: Heatmap with all pairwise D' values
  • <prefix>_R2.pdf: Heatmap with all pairwise R^2 values
  • <prefix>_Dc_sig.pdf: Heatmap with the pairwise D' values of the statistically significant pairs
  • <prefix>_R2_sig.pdf: Heatmap with the pairwise R^2 values of the statistically significant pairs
  • <prefix>_Dc_hist.pdf: Histogram with the distribution of D' values
  • <prefix>_R2_hist.pdf: Histogram with the distribution of R^2 values
  • <prefix>_pval.pdf: Heatmap with the pairwise LD p-values.
  • <prefix>_qval.pdf: Heatmap with the FDR corrected pairwise LD p-values.
  • <prefix>.log: Text file with summary information about the LD results
  • Significant_snp_pairs.csv: Tabular file with a list of the statistically significant SNP pairs.

Output examples

Heatmap of pairwise D' for all SNPs

Heatmap of pairwise D' for statistically significant SNP pairs

Distribution of pairwise D' values