How can find LD between rows (SNPs) two by two?
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8.2 years ago
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I like to find linkage Disequilibrium (LD) between my positions (rows). I have used SNPRelate package for finding LD as below but I want compare each row with others as I show in out put.

snp1<-as.numeric(c("0","1","1","2"))
snp2<-as.numeric(c("NA","1","2","1"))
Warning message:
NAs introduced by coercion

LD<-snpgdsLDpair(snp1,snp2,"dprime")

LD
ld pA_A pA_B pB_A pB_B
9.999998e-01 3.333334e-01 3.333333e-01 3.333333e-01 2.554527e-08

Input:

pos sample1 sample2 sample3 sample4
SNP1 0 1 1 2
SNP2 NA 1 2 1
SNP3 2 2 0 1
SNP4 0 1 1 2

Each samples code as(NA = no read data , 0 = Homozygous Reference genotype , 1 = Heterozygous genotype and 2 = Homozygous Alternative genotype )

Output:

ld
SNP1 SNP2 0.25
SNP1 SNP3 0.36
SNP1 SNP4 0.54
SNP2 SNP3 0.33
SNP2 SNP4 0.36
SNP3 SNP4 0.69

Value of ld in above in output is not accurate.

linkage-Disequilibrium genomics R • 2.1k views
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I usually use the genetics package. The input is similar to yours, but you have to specify a genotype explicitly (i.e. A/A, A/T, T/T) instead of 0,1,2. However, the manual is rather exhaustive. In genetics, using LD(mydata) will perform all the pairwise comparisons.

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Dear Fabio,

Thanks for your help.

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