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How to assign LD proxy

Bioinformatics Asked on April 28, 2021

When we use local data using TwoSampleMR, how can we assign LD proxies where the outcome data is not available?

https://mrcieu.github.io/TwoSampleMR/articles/outcome.html

  outcome_dat <- read_outcome_data(
   snps = bmi_exp_dat$SNP,
   filename = "gwas_summary.csv",
   sep = ",",
   snp_col = "rsid",
   beta_col = "effect",
    se_col = "SE",
  effect_allele_col = "a1",
   other_allele_col = "a2",
  eaf_col = "a1_freq",
  pval_col = "p-value",
   units_col = "Units",
  gene_col = "Gene",
  samplesize_col = "n"
  )

When we use "extract_outcome_data", we can automatically assign LD proxies, but this cannot be applied to local data.

   chd_out_dat <- extract_outcome_data(
    snps = bmi_exp_dat$SNP,
    outcomes = 'ieu-a-7'
    )
#> Extracting data for 79 SNP(s) from 1 GWAS(s)

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