Hello, I have my genetic data in *.bim *.bed and *.fam format. I have a *.txt file containing the SNPs of my interest. I want to estimate pairwise linkage disequilibrium (LD) among all of the SNPs in that Text file. I want to obtain the LD r2 values both as a list and a square matrix format. I have used the following codes for the list and matrix format, respectively:

plink --bfile plink_binary.0 --allow-no-sex --extract file.txt --r2 --out file
plink --bfile plink_binary.0 --extract file.txt --r2 square --write-snplist --out file

Both of them produce the desire results. However, there is a discrepancy between the two output files. I used output which is in List format in R and used the dcast function to convert the list into a matrix format. So that I can plot the LD heatmap. When I want to do that, I cannot produce the LD heatmap and shows the error that it is not a square matrix. But if I used the matrix output from PLINK then everything is fine. However, the matrix from PLINK and the matrix from R is not the same. I see that in the List output format there is a SNP that is not present (may be it has no LD or very low LD). But I am not sure whether that SNP is omitted when PLINK produce the output as a matrix. Because in the matrix output, the name of the SNPs are not printed.

Does anyone have any ideas on what is wrong here? Any suggestions will be appreciated. Thank you.