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运行 2_linkage_disequilibrium_analysis,报错:
`Clumping q7JdGx, 995 variants, using EUR population reference
Error in get_plink_exe() : 没有"get_plink_exe"这个函数`
加入:
`library(plinkbinr)`
成功运行2_linkag…
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Thank you for your tutorial in advance.
I have some confusion about the "inversion.txt" in the 1_QC_GWAS folder. I know it is for excluding high inversion regions. However, where is the "inversion.tx…
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The locus drawer will open from the number field in the `credible set size` column, for both GWAS and molQTLs widget.
if credible sets size is 7, the drawer will contain 7 rows for 7 variants in the …
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### A clear description of your feature request
Calculation of linkage disequilibrium via phased data and comparing phased and unphased LD via a Sign test. Also for 2-locus haplotypes, calculation of…
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Do you recommend pruning SNPs that are in linkage disequilibrium before feeding into varbvs? It looks like paper suggests that the variational approximation works better under independence of the SNPs…
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Need R code to test linkage disequilibrium between TE variants and flanking SNPs
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**Please describe your question, suggestion, or concern.**
How is "correlated disease" used in Monarch?
I can't see where this is defined.
I had assumed it was used when a variant is correlated…
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This should help with some sampling related issues and also preserve some degree of linkage disequilibrium. The block size could be an input argument.
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I noticed that you have a script called get_SNP_STR_LD.v2.py for calculating linkage disequilibrium (LD) between str and snp. Could you provide an example format for the str? I happen to be dealing wi…
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Hi, i have the same problem.
I want to perform rare variants (MAF < 1%) analysis in Regenie, and have tried many times to follow your earlier advice to others, but still encounter the s…