I have a bunch of CNVs which I have estimated LD between each allele of CNV with all SNPs across the entire human genome. I used my R-script to do a pairwise LD analysis.

The following is the first few lines of my output for the first alternative allele of CNV and some SNPs on chromosome 2 (just as an example)

CNV_chrom  CNV_allele  SNP_chrom  SNP_position  R2
"1" "  CNV2"   "2"        " 1000"    "-0.0463767871013283" 
"1" "  CNV2"   "2"        " 1029"    "-0.201478578143067" 
"1" "  CNV2"   "2"        " 1044"    "-0.595441932439136"
"1" "  CNV2"   "2"        " 1045"    "-0.60363963711489"
"1" "  CNV2"   "2"        " 1130"    "0.377970958849221" 

I want to plot the LD results (LD between each allele of CNV and all SNPs) ,is there any way that I could do it in R?

I have not done LD plotting before so just slightly confused.

I saw for instance LDheatmap package in R, but do not know how can I summarize the results for thousands of SNPs. Thanks for any suggestion

Summary of LDHeatmap

Produces a graphical display, as a heat map, of measures of pairwise linkage disequilibria between single nucleotide polymorphisms (SNPs). Users may optionally include the physical locations or genetic map distances of each SNP on the plot.


Shin, J.-H., Blay, S., McNeney, B., & Graham, J. (2006). LDheatmap: An R Function for Graphical Display of Pairwise Linkage Disequilibria Between Single Nucleotide Polymorphisms. Journal of Statistical Software, Code Snippets, 16(3), 1–9. https://doi.org/10.18637/jss.v016.c03



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