there is no LD information of loci in my plot

[lzhao42]

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) 

Can you help me see why？

[whweve]

can you please send me some demo data for me to try? thanks

---- 回复的原邮件 ---- | 发件人 | @.> | | 日期 | 2021年12月09日 17:51 | | 收件人 | @.> | | 抄送至 | @.***> | | 主题 | [whweve/IntAssoPlot] there is no LD information of loci in my plot (Issue #7) |

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)

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android.

[lzhao42]

I am very sorry that unpublished data cannot be sent to others without permission. My data are whole genome sequences, with missing rate of every SNP less than 5%.