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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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Hello,
Thank you very much for a nice package!
My question is: can one use allelefrequencies data to calculate relative usage of different loci in a population or ethnic group? Does it actually …
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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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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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Hi Doug,
I am running into an error when LDAK is reading in the covariates file. I've tried changing the file from tab to space separated, removing any non-alphanumeric values from the variable nam…
sahwa updated
1 month ago
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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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We are running the latest LDAK6 in a Red Hat 8.8 cluster, using the Slurm scheduler. When the job runs, we get the following output:
(base) [laip@esplhpccompbio-lv01 MegaPRS]$ cat JOB1003351.out
…
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Need R code to test linkage disequilibrium between TE variants and flanking SNPs
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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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When I made the locuszoom plot, I found that there was no LD information of the locus in…