Hi everyone!
I have a dataset of SNPs along chromosomes (physical positions are available) of several individuals from natural populations. I'm now interested in calculating LD along these chromosomes based on these unphased SNPs. So basically I want to only look at LD (e.g., by calculating R^2) between neighboring SNPs, such as 1/2, 2/3, 3/4 ...
Is there an R package available for this?
I thought about using Plink, but it seems that PLINK only handles pedigree data, right? Of course, I don't know about that as my individuals were sampled in nature.
Thank you for your help!
I have a dataset of SNPs along chromosomes (physical positions are available) of several individuals from natural populations. I'm now interested in calculating LD along these chromosomes based on these unphased SNPs. So basically I want to only look at LD (e.g., by calculating R^2) between neighboring SNPs, such as 1/2, 2/3, 3/4 ...
Is there an R package available for this?
I thought about using Plink, but it seems that PLINK only handles pedigree data, right? Of course, I don't know about that as my individuals were sampled in nature.
Thank you for your help!
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