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.
SNPair_LD.R requires the following libraries:
- pegas
- fields
- genetics
- reshape2
- ggplot2
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.
