4.5 Counting haplotypes with table

We can use the table function to count the occurrence of the four possible haplotypes.

table(haplotypes$snp1_allele, haplotypes$snp2_allele)

##    
##        C    T
##   A 2655  801
##   G  170 1382

The table tells us that there are 2655 A C haplotypes (A at SNP1 and C at SNP2), 170 G C haplotypes, etc.

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Do these SNPs look like they’re in LD?

It looks like there are some haplotypes (A C and G T) that are overrepresented. However, it’s hard to tell whether that’s just because an A allele at SNP1 is much more common than T is.

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