I have generated the linkage disequilibrium results using TASSEL and want to produce LD-decay plot using R for different chromosomes. I am looking for the data format and R script to generate same.
@Leandro, Thank you so much for your suggestion. It was really helpful.
Hello,
I have two suggestions:
1- Since Tassel can give r2 as linkage disequilibrium between two markers or two regions, you can simply plot r2s in the Y-axis vs distance in the X-axis which depicts how r2 decreases by increasing in marker distance as a scatter plot.
2- Also LDkit can use both VCF and PLINK formats. At the same time, you could also just analyze a subset of individuals or a subset of the genomic regions (chromosome) for either LD decay and LD-Block analyzes.
Good luck
Since Tassel can give r2 as linkage disequilibrium between two markers or two regions, you can simply plot r2s in the Y-axis vs distance in the X-axis which depicts how r2 decreases by increasing in marker distance as a scatter plot.
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