When I made the locuszoom plot, I found that there was no LD information of the locus in my plot.
IntRegionalPlot(chr = chr,left =pos-10000,right =pos+10000,gtf = locus_zoom_gtf,leadsnpLD = TRUE,association = locus_zoom_snp,hapmap = locus_zoom_genotype,hapmap_ld = locus_zoom_genotype,threshold = 5,leadsnp_size = 2,label_gene_name = T,threadN = 10)
Linkage Disequilibrium (LD) estimation on genotypes:
Working space: 133 samples, 35 SNPs
using 10 (CPU) cores.
method: correlation
LD matrix: the sum of all selected genotypes (0,1,2) = 6820
Linkage Disequilibrium (LD) estimation on genotypes:
Working space: 133 samples, 35 SNPs
using 10 (CPU) cores.
method: correlation
LD matrix: the sum of all selected genotypes (0,1,2) = 6820
There were 50 or more warnings (use warnings() to see the first 50)
When I made the locuszoom plot, I found that there was no LD information of the locus in my plot.
Can you help me see why？